3FYU | pdb_00003fyu

Crystal structure of acetyl xylan esterase from Bacillus pumilus obtained in presence of D-xylose and sodium acetate

PDB DOI: https://doi.org/10.2210/pdb3FYU/pdb

Classification: HYDROLASE
Organism(s): Bacillus pumilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-23 Released: 2010-01-26
Deposition Author(s): Krastanova, I., Cassetta, A., Lamba, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.230 (Depositor), 0.220 (DCC)
R-Value Work:
0.196 (Depositor), 0.180 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structural and functional studies of Bacillus pumilus acetyl xylan esterase

Krastanova, I., Cassetta, A., Mastihubova, M., Biely, P., Lamba, D.

To be published.

Macromolecule Content

Total Structure Weight: 436.44 kDa
Atom Count: 31,382
Modeled Residue Count: 3,800
Deposited Residue Count: 3,840
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl xylan esterase	A, I	320	Bacillus pumilus	Mutation(s): 0 Gene Names: axe EC: 3.1.1.6
UniProt
Find proteins for Q9K5F2 (Bacillus pumilus) Explore Q9K5F2 Go to UniProtKB: Q9K5F2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K5F2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl xylan esterase	B, D, H	320	Bacillus pumilus	Mutation(s): 0 Gene Names: axe EC: 3.1.1.6
UniProt
Find proteins for Q9K5F2 (Bacillus pumilus) Explore Q9K5F2 Go to UniProtKB: Q9K5F2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K5F2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl xylan esterase	C E F G J [auth L] C, E, F, G, J [auth L], K [auth M], L [auth N]	320	Bacillus pumilus	Mutation(s): 0 Gene Names: axe EC: 3.1.1.6
UniProt
Find proteins for Q9K5F2 (Bacillus pumilus) Explore Q9K5F2 Go to UniProtKB: Q9K5F2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K5F2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYP Query on XYP Download Ideal Coordinates CCD File SDF format, chain ZA [auth N] SDF format, chain WA [auth M] SDF format, chain UA [auth L] SDF format, chain U [auth C] SDF format, chain RA [auth I] SDF format, chain M [auth A] SDF format, chain BA [auth E] MOL2 format, chain ZA [auth N] MOL2 format, chain WA [auth M] MOL2 format, chain UA [auth L] MOL2 format, chain U [auth C] MOL2 format, chain RA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain BA [auth E] mmCIF format, chain ZA [auth N] mmCIF format, chain WA [auth M] mmCIF format, chain UA [auth L] mmCIF format, chain U [auth C] mmCIF format, chain RA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain BA [auth E]	BA [auth E] M [auth A] RA [auth I] U [auth C] UA [auth L] BA [auth E], M [auth A], RA [auth I], U [auth C], UA [auth L], WA [auth M], ZA [auth N]	beta-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-KKQCNMDGSA-N		Interactions Focus chain BA [auth E] Focus chain M [auth A] Focus chain RA [auth I] Focus chain U [auth C] Focus chain UA [auth L] Focus chain WA [auth M] Focus chain ZA [auth N] Interactions & Density Focus chain BA [auth E] Focus chain M [auth A] Focus chain RA [auth I] Focus chain U [auth C] Focus chain UA [auth L] Focus chain WA [auth M] Focus chain ZA [auth N]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth N] SDF format, chain R [auth B] SDF format, chain Y [auth D] SDF format, chain XA [auth M] SDF format, chain X [auth D] SDF format, chain SA [auth I] SDF format, chain Q [auth B] SDF format, chain NA [auth H] SDF format, chain N [auth A] SDF format, chain KA [auth G] SDF format, chain HA [auth F] SDF format, chain GA [auth F] SDF format, chain CA [auth E] MOL2 format, chain AB [auth N] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain XA [auth M] MOL2 format, chain X [auth D] MOL2 format, chain SA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain NA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain HA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain AB [auth N] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain XA [auth M] mmCIF format, chain X [auth D] mmCIF format, chain SA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain NA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain HA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain CA [auth E]	AB [auth N] CA [auth E] GA [auth F] HA [auth F] KA [auth G] AB [auth N], CA [auth E], GA [auth F], HA [auth F], KA [auth G], N [auth A], NA [auth H], Q [auth B], R [auth B], SA [auth I], X [auth D], XA [auth M], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth N] Focus chain CA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain N [auth A] Focus chain NA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth I] Focus chain X [auth D] Focus chain XA [auth M] Focus chain Y [auth D] Interactions & Density Focus chain AB [auth N] Focus chain CA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain N [auth A] Focus chain NA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth I] Focus chain X [auth D] Focus chain XA [auth M] Focus chain Y [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain QA [auth I] SDF format, chain JA [auth G] SDF format, chain FA [auth F] SDF format, chain AA [auth E] MOL2 format, chain T [auth C] MOL2 format, chain QA [auth I] MOL2 format, chain JA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain T [auth C] mmCIF format, chain QA [auth I] mmCIF format, chain JA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain AA [auth E]	AA [auth E], FA [auth F], JA [auth G], QA [auth I], T [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain JA [auth G] Focus chain QA [auth I] Focus chain T [auth C] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain JA [auth G] Focus chain QA [auth I] Focus chain T [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain YA [auth M] SDF format, chain W [auth C] SDF format, chain VA [auth L] SDF format, chain V [auth C] SDF format, chain TA [auth I] SDF format, chain S [auth B] SDF format, chain PA [auth H] SDF format, chain P [auth A] SDF format, chain OA [auth H] SDF format, chain O [auth A] SDF format, chain MA [auth G] SDF format, chain LA [auth G] SDF format, chain IA [auth F] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CB [auth N] SDF format, chain BB [auth N] MOL2 format, chain Z [auth D] MOL2 format, chain YA [auth M] MOL2 format, chain W [auth C] MOL2 format, chain VA [auth L] MOL2 format, chain V [auth C] MOL2 format, chain TA [auth I] MOL2 format, chain S [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain IA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CB [auth N] MOL2 format, chain BB [auth N] mmCIF format, chain Z [auth D] mmCIF format, chain YA [auth M] mmCIF format, chain W [auth C] mmCIF format, chain VA [auth L] mmCIF format, chain V [auth C] mmCIF format, chain TA [auth I] mmCIF format, chain S [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain IA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CB [auth N] mmCIF format, chain BB [auth N]	BB [auth N] CB [auth N] DA [auth E] EA [auth E] IA [auth F] BB [auth N], CB [auth N], DA [auth E], EA [auth E], IA [auth F], LA [auth G], MA [auth G], O [auth A], OA [auth H], P [auth A], PA [auth H], S [auth B], TA [auth I], V [auth C], VA [auth L], W [auth C], YA [auth M], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BB [auth N] Focus chain CB [auth N] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain PA [auth H] Focus chain S [auth B] Focus chain TA [auth I] Focus chain V [auth C] Focus chain VA [auth L] Focus chain W [auth C] Focus chain YA [auth M] Focus chain Z [auth D] Interactions & Density Focus chain BB [auth N] Focus chain CB [auth N] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain PA [auth H] Focus chain S [auth B] Focus chain TA [auth I] Focus chain V [auth C] Focus chain VA [auth L] Focus chain W [auth C] Focus chain YA [auth M] Focus chain Z [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OAS Query on OAS	A, I	L-PEPTIDE LINKING	C₅ H₉ N O₄		SER
TIS Query on TIS	B, D, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₅		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.230 (Depositor), 0.220 (DCC)
R-Value Work: 0.196 (Depositor), 0.180 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.225	α = 90
b = 86.622	β = 112.78
c = 183.973	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-01-26

Deposition Author(s):

Krastanova, I.

Cassetta, A.

Lamba, D.

Revision History (Full details and data files)

Version 1.0: 2010-01-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2023-11-22
Changes: Data collection, Derived calculations