3DAS | pdb_00003das

Structure of the PQQ-bound form of Aldose Sugar Dehydrogenase (Adh) from Streptomyces coelicolor

PDB DOI: https://doi.org/10.2210/pdb3DAS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces coelicolor
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-30 Released: 2009-06-02
Deposition Author(s): Southall, S.M., Doel, J.J., Oubrie, A., Richardson, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.159 (Depositor), 0.158 (DCC)
R-Value Work:
0.132 (Depositor), 0.132 (DCC)
R-Value Observed:
0.134 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and Enzymatic Characterization of a Thermostable PQQ-dependent Soluble Aldose Sugar Dehydrogenase

Southall, S.M., Doel, J.J., Oubrie, A., Richardson, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 38 kDa
Atom Count: 3,339
Modeled Residue Count: 334
Deposited Residue Count: 347
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A	347	Streptomyces coelicolor	Mutation(s): 0
UniProt
Find proteins for Q9Z571 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9Z571 Go to UniProtKB: Q9Z571
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Z571
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PQQ Query on PQQ Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PYRROLOQUINOLINE QUINONE C₁₄ H₆ N₂ O₈ MMXZSJMASHPLLR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ARA Query on ARA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	alpha-L-arabinopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-QMKXCQHVSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.159 (Depositor), 0.158 (DCC)
R-Value Work: 0.132 (Depositor), 0.132 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.033	α = 90
b = 41.26	β = 93.58
c = 85.931	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
MLPHARE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-06-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-02
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: 2024-10-30
Changes: Data collection, Database references, Structure summary

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Structure of the PQQ-bound form of Aldose Sugar Dehydrogenase (Adh) from Streptomyces coelicolor

Structural and Enzymatic Characterization of a Thermostable PQQ-dependent Soluble Aldose Sugar Dehydrogenase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations