4HP8

Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from Agrobacterium Tumefaciens (target EFI-506435) with bound NADP

PDB DOI: https://doi.org/10.2210/pdb4HP8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-10-23 Released: 2012-11-07
Deposition Author(s): Vetting, M.W., Bouvier, J.T., Groninger-Poe, F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.156
R-Value Work: 0.139
R-Value Observed: 0.140

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from Agrobacterium Tumefaciens (target EFI-506435) with bound NADP

Vetting, M.W., Bouvier, J.T., Groninger-Poe, F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 53.09 kDa
Atom Count: 4,371
Modelled Residue Count: 491
Deposited Residue Count: 494
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-deoxy-D-gluconate 3-dehydrogenase	A, B	247	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: kduD, Atu3141
UniProt
Find proteins for A9CEQ9 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CEQ9 Go to UniProtKB: A9CEQ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9CEQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.156
R-Value Work: 0.139
R-Value Observed: 0.140
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.022	α = 90
b = 93.022	β = 90
c = 109.285	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4HP8

Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from Agrobacterium Tumefaciens (target EFI-506435) with bound NADP

Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from Agrobacterium Tumefaciens (target EFI-506435) with bound NADP

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)