2Z1M

Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5

PDB DOI: https://doi.org/10.2210/pdb2Z1M/pdb

Classification: LYASE
Organism(s): Aquifex aeolicus VF5
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-05-09 Released: 2007-11-13
Deposition Author(s): Niwa, H., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5

Niwa, H., Kuramitsu, S., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 159.93 kDa
Atom Count: 11,393
Modelled Residue Count: 1,344
Deposited Residue Count: 1,380
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-D-mannose dehydratase	A, B, C, D	345	Aquifex aeolicus VF5	Mutation(s): 0 Gene Names: rfbD EC: 4.2.1.47
UniProt
Find proteins for O67175 (Aquifex aeolicus (strain VF5)) Explore O67175 Go to UniProtKB: O67175
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O67175
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth D]	E [auth A], G [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth D]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth D]	F [auth A], H [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain H [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.799	α = 90
b = 151.164	β = 108.6
c = 85.934	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-11-13

Deposition Author(s):

Niwa, H.

Kuramitsu, S.

Yokoyama, S.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-11-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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2Z1M

Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5

Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5

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)