3ACT | pdb_00003act

Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase Histidine mutant

PDB DOI: https://doi.org/10.2210/pdb3ACT/pdb

Classification: TRANSFERASE
Organism(s): Cellulomonas gilvus ATCC 13127
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-01-08 Released: 2010-12-22
Deposition Author(s): Hidaka, M., Hayashi, M.A., Fushinobu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.176 (Depositor), 0.180 (DCC)
R-Value Work:
0.128 (Depositor), 0.130 (DCC)
R-Value Observed:
0.131 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Engineering of cellobiose phosphorylase

Arai, T., Hayashi, M.A., Hidaka, M., Kitaoka, M., Wakagi, T., Shoun, H., Fushinobu, S.

To be published.

Macromolecule Content

Total Structure Weight: 187.18 kDa
Atom Count: 15,120
Modeled Residue Count: 1,644
Deposited Residue Count: 1,684
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiose Phosphorylase	A, B	842	Cellulomonas gilvus ATCC 13127	Mutation(s): 1 EC: 2.4.1.20
UniProt
Find proteins for O66264 (Cellulomonas gilvus) Explore O66264 Go to UniProtKB: O66264
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O66264
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth B]	F [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.176 (Depositor), 0.180 (DCC)
R-Value Work: 0.128 (Depositor), 0.130 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.36	α = 90
b = 98.315	β = 102.72
c = 104.332	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-12-22

Deposition Author(s):

Hidaka, M.

Hayashi, M.A.

Fushinobu, S.

Revision History (Full details and data files)

Version 1.0: 2010-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary

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Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase Histidine mutant

Engineering of cellobiose phosphorylase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations