2X5K | pdb_00002x5k

Structure of an active site mutant of the D-Erythrose-4-Phosphate Dehydrogenase from E. coli

PDB DOI: https://doi.org/10.2210/pdb2X5K/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2010-02-10 Released: 2011-02-16
Deposition Author(s): Moniot, S., Didierjean, C., Boschi-Muller, S., Branlant, G., Corbier, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.207 (Depositor), 0.210 (DCC)
R-Value Work:
0.164 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 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: 151.17 kDa
Atom Count: 11,575
Modelled Residue Count: 1,342
Deposited Residue Count: 1,356
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE	A [auth O], B [auth P], C [auth Q], D [auth R]	339	Escherichia coli K-12	Mutation(s): 2 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A9B6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain H [auth O] MOL2 format, chain H [auth O] mmCIF format, chain H [auth O]	H [auth O]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth O] Interactions & Density Focus chain H [auth O]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain J [auth O] SDF format, chain Q [auth P] SDF format, chain R [auth P] SDF format, chain U [auth Q] MOL2 format, chain J [auth O] MOL2 format, chain Q [auth P] MOL2 format, chain R [auth P] MOL2 format, chain U [auth Q] mmCIF format, chain J [auth O] mmCIF format, chain Q [auth P] mmCIF format, chain R [auth P] mmCIF format, chain U [auth Q]	J [auth O], Q [auth P], R [auth P], U [auth Q]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth O] Focus chain Q [auth P] Focus chain R [auth P] Focus chain U [auth Q] Interactions & Density Focus chain J [auth O] Focus chain Q [auth P] Focus chain R [auth P] Focus chain U [auth Q]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain O [auth P] SDF format, chain P MOL2 format, chain O [auth P] MOL2 format, chain P mmCIF format, chain O [auth P] mmCIF format, chain P	O [auth P], P	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain O [auth P] Focus chain P Interactions & Density Focus chain O [auth P] Focus chain P
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth O] SDF format, chain F [auth O] SDF format, chain K [auth P] SDF format, chain L [auth P] SDF format, chain W [auth R] SDF format, chain X [auth R] MOL2 format, chain E [auth O] MOL2 format, chain F [auth O] MOL2 format, chain K [auth P] MOL2 format, chain L [auth P] MOL2 format, chain W [auth R] MOL2 format, chain X [auth R] mmCIF format, chain E [auth O] mmCIF format, chain F [auth O] mmCIF format, chain K [auth P] mmCIF format, chain L [auth P] mmCIF format, chain W [auth R] mmCIF format, chain X [auth R]	E [auth O] F [auth O] K [auth P] L [auth P] W [auth R] E [auth O], F [auth O], K [auth P], L [auth P], W [auth R], X [auth R]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth O] Focus chain F [auth O] Focus chain K [auth P] Focus chain L [auth P] Focus chain W [auth R] Focus chain X [auth R] Interactions & Density Focus chain E [auth O] Focus chain F [auth O] Focus chain K [auth P] Focus chain L [auth P] Focus chain W [auth R] Focus chain X [auth R]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth O] SDF format, chain M [auth P] SDF format, chain S [auth Q] SDF format, chain T [auth Q] SDF format, chain Y [auth R] MOL2 format, chain G [auth O] MOL2 format, chain M [auth P] MOL2 format, chain S [auth Q] MOL2 format, chain T [auth Q] MOL2 format, chain Y [auth R] mmCIF format, chain G [auth O] mmCIF format, chain M [auth P] mmCIF format, chain S [auth Q] mmCIF format, chain T [auth Q] mmCIF format, chain Y [auth R]	G [auth O], M [auth P], S [auth Q], T [auth Q], Y [auth R]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth O] Focus chain M [auth P] Focus chain S [auth Q] Focus chain T [auth Q] Focus chain Y [auth R] Interactions & Density Focus chain G [auth O] Focus chain M [auth P] Focus chain S [auth Q] Focus chain T [auth Q] Focus chain Y [auth R]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth O] SDF format, chain N [auth P] SDF format, chain V [auth Q] MOL2 format, chain I [auth O] MOL2 format, chain N [auth P] MOL2 format, chain V [auth Q] mmCIF format, chain I [auth O] mmCIF format, chain N [auth P] mmCIF format, chain V [auth Q]	I [auth O], N [auth P], V [auth Q]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth O] Focus chain N [auth P] Focus chain V [auth Q] Interactions & Density Focus chain I [auth O] Focus chain N [auth P] Focus chain V [auth Q]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.207 (Depositor), 0.210 (DCC)
R-Value Work: 0.164 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.81	α = 90
b = 134.81	β = 90
c = 246.11	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-02-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-02-16
Type: Initial release
Version 1.1: 2011-05-08
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