2XF8 | pdb_00002xf8

Structure of the D-Erythrose-4-Phosphate Dehydrogenase from E. coli in complex with a NAD cofactor analog (3-Chloroacetyl adenine pyridine dinucleotide) and sulfate anion

PDB DOI: https://doi.org/10.2210/pdb2XF8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2010-05-20 Released: 2011-06-08
Deposition Author(s): Moniot, S., Didierjean, C., Boschi-Muller, S., Branlant, G., Corbier, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.280 (Depositor), 0.275 (DCC)
R-Value Work:
0.237 (Depositor), 0.234 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Characterization of Erythrose-4- Phosphate Dehydrogenase from Escherichia Coli: Peculiar Features When Compared to Phosphorylating Gapdhs

Moniot, S., Didierjean, C., Boschi-Muller, S., Branlant, G., Corbier, C.

To be published.

Macromolecule Content

Total Structure Weight: 602.58 kDa
Atom Count: 40,244
Modeled Residue Count: 5,156
Deposited Residue Count: 5,408
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	338	Escherichia coli K-12	Mutation(s): 0 EC: 1.2.1.72
UniProt
Find proteins for P0A9B6 (Escherichia coli (strain K12)) Explore P0A9B6 Go to UniProtKB: P0A9B6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A9B6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3CD Query on 3CD Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain U [auth C] SDF format, chain R [auth A] SDF format, chain MA [auth O] SDF format, chain JA [auth M] SDF format, chain GA [auth K] SDF format, chain DA [auth I] SDF format, chain AA [auth G] MOL2 format, chain X [auth E] MOL2 format, chain U [auth C] MOL2 format, chain R [auth A] MOL2 format, chain MA [auth O] MOL2 format, chain JA [auth M] MOL2 format, chain GA [auth K] MOL2 format, chain DA [auth I] MOL2 format, chain AA [auth G] mmCIF format, chain X [auth E] mmCIF format, chain U [auth C] mmCIF format, chain R [auth A] mmCIF format, chain MA [auth O] mmCIF format, chain JA [auth M] mmCIF format, chain GA [auth K] mmCIF format, chain DA [auth I] mmCIF format, chain AA [auth G]	AA [auth G] DA [auth I] GA [auth K] JA [auth M] MA [auth O] AA [auth G], DA [auth I], GA [auth K], JA [auth M], MA [auth O], R [auth A], U [auth C], X [auth E]	3-(CHLOROACETYL) PYRIDINE ADENINE DINUCLEOTIDE C₂₂ H₂₈ Cl N₆ O₁₄ P₂ XIQCGHNADRRDKB-RBEMOOQDSA-O		Interactions Focus chain AA [auth G] Focus chain DA [auth I] Focus chain GA [auth K] Focus chain JA [auth M] Focus chain MA [auth O] Focus chain R [auth A] Focus chain U [auth C] Focus chain X [auth E] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth I] Focus chain GA [auth K] Focus chain JA [auth M] Focus chain MA [auth O] Focus chain R [auth A] Focus chain U [auth C] Focus chain X [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain Y [auth F] SDF format, chain W [auth E] SDF format, chain V [auth D] SDF format, chain T [auth C] SDF format, chain S [auth B] SDF format, chain Q [auth A] SDF format, chain NA [auth P] SDF format, chain LA [auth O] SDF format, chain KA [auth N] SDF format, chain IA [auth M] SDF format, chain HA [auth L] SDF format, chain FA [auth K] SDF format, chain EA [auth J] SDF format, chain CA [auth I] SDF format, chain BA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain W [auth E] MOL2 format, chain V [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain NA [auth P] MOL2 format, chain LA [auth O] MOL2 format, chain KA [auth N] MOL2 format, chain IA [auth M] MOL2 format, chain HA [auth L] MOL2 format, chain FA [auth K] MOL2 format, chain EA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain W [auth E] mmCIF format, chain V [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain NA [auth P] mmCIF format, chain LA [auth O] mmCIF format, chain KA [auth N] mmCIF format, chain IA [auth M] mmCIF format, chain HA [auth L] mmCIF format, chain FA [auth K] mmCIF format, chain EA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth H]	BA [auth H] CA [auth I] EA [auth J] FA [auth K] HA [auth L] BA [auth H], CA [auth I], EA [auth J], FA [auth K], HA [auth L], IA [auth M], KA [auth N], LA [auth O], NA [auth P], Q [auth A], S [auth B], T [auth C], V [auth D], W [auth E], Y [auth F], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain IA [auth M] Focus chain KA [auth N] Focus chain LA [auth O] Focus chain NA [auth P] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain IA [auth M] Focus chain KA [auth N] Focus chain LA [auth O] Focus chain NA [auth P] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.280 (Depositor), 0.275 (DCC)
R-Value Work: 0.237 (Depositor), 0.234 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.18	α = 91.3
b = 111.66	β = 96.11
c = 135.47	γ = 88.44

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-06-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-08
Type: Initial release
Version 1.1: 2011-06-09
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary