1G6K

Crystal structure of glucose dehydrogenase mutant E96A complexed with NAD+

PDB DOI: https://doi.org/10.2210/pdb1G6K/pdb

Classification: OXIDOREDUCTASE
Organism(s): Priestia megaterium
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2000-11-06 Released: 2003-08-12
Deposition Author(s): Yamamoto, K., Kurisu, G., Kusunoki, M., Tabata, S., Urabe, I., Osaki, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.238
R-Value Work: 0.219

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural analysis of stability-increasing mutants of glucose dehydrogenase

Yamamoto, K., Kurisu, G., Kusunoki, M., Tabata, S., Urabe, I., Osaki, S.

To be published.

Macromolecule Content

Total Structure Weight: 114.87 kDa
Atom Count: 8,359
Modelled Residue Count: 1,044
Deposited Residue Count: 1,044
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSE 1-DEHYDROGENASE	A, B, C [auth E], D [auth F]	261	Priestia megaterium	Mutation(s): 1 EC: 1.1.1.47
UniProt
Find proteins for P40288 (Priestia megaterium) Explore P40288 Go to UniProtKB: P40288
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40288
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain G [auth E] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain H [auth F] MOL2 format, chain G [auth E] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth F] mmCIF format, chain G [auth E] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth F]	E [auth A], F [auth B], G [auth E], H [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth E] Focus chain H [auth F] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth E] Focus chain H [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.238
R-Value Work: 0.219
Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 121.955	α = 90
b = 66.64	β = 93.44
c = 120.065	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-08-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-08-12
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-10-25
Changes: Data collection, Refinement description

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1G6K

Crystal structure of glucose dehydrogenase mutant E96A complexed with NAD+

Structural analysis of stability-increasing mutants of glucose dehydrogenase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)