7ANJ | pdb_00007anj

DdahB, GDP-mannoheptose C3,5 epimerase from Campylobacter jejuni complexed to GDP-mannose

PDB DOI: https://doi.org/10.2210/pdb7ANJ/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-10-11 Released: 2020-10-21
Deposition Author(s): Naismith, J.H., Woodward, L.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.244 (Depositor), 0.255 (DCC)
R-Value Work:
0.185 (Depositor), 0.194 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

DdhaB with GDP-mannose

Naismith, J.H., Woodward, L.

To be published.

Macromolecule Content

Total Structure Weight: 42.96 kDa
Atom Count: 2,855
Modeled Residue Count: 335
Deposited Residue Count: 366
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine diphospho-4-keto-rhamnose 3,5-epimerase	A, B	183	Campylobacter jejuni	Mutation(s): 0 Gene Names: BBR99_05345, D0W34_08620, D5I02_08520, F0H18_08555, F1P94_09915, FRS42_06315, FVZ69_07850, FW031_08545, FW918_03925, FWZ96_07945... BBR99_05345, D0W34_08620, D5I02_08520, F0H18_08555, F1P94_09915, FRS42_06315, FVZ69_07850, FW031_08545, FW918_03925, FWZ96_07945, GAX04_08395, GJ442_08190, GRS20_08795, GSH24_04195, GY415_001377, GZD82_001464, HS23.15 EC: 5.1.3.13
UniProt
Find proteins for Q6EF58 (Campylobacter jejuni) Explore Q6EF58 Go to UniProtKB: Q6EF58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6EF58
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDD Query on GDD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE C₁₆ H₂₅ N₅ O₁₆ P₂ MVMSCBBUIHUTGJ-GDJBGNAASA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.244 (Depositor), 0.255 (DCC)
R-Value Work: 0.185 (Depositor), 0.194 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.001	α = 90
b = 67.81	β = 91.79
c = 53.14	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	100209/Z/12/Z)

Revision History (Full details and data files)

Version 1.0: 2020-10-21
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.