6K0K

Crystal structure of Escherichia coli pyruvate kinase II

PDB DOI: https://doi.org/10.2210/pdb6K0K/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-07 Released: 2020-05-13
Deposition Author(s): Zhao, C.H., Zhang, Y.P., Li, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.259
R-Value Work: 0.210
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Escherichia coli pyruvate kinase II

Zhao, C.H., Zhang, Y.P., Li, Y.

To be published.

Macromolecule Content

Total Structure Weight: 210.64 kDa
Atom Count: 13,318
Modelled Residue Count: 1,746
Deposited Residue Count: 1,956
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B, C, D	489	Escherichia coli	Mutation(s): 0 EC: 2.7.1.40
UniProt
Find proteins for P21599 (Escherichia coli (strain K12)) Explore P21599 Go to UniProtKB: P21599
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21599
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D]	F [auth A], I [auth C], K [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth C] Focus chain K [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D]	E [auth A], G [auth C], H [auth C], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth C] Focus chain H [auth C] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.259
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.693	α = 90
b = 137.3	β = 90
c = 139.221	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Zhao, C.H.

Zhang, Y.P.

Li, Y.

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

6K0K

Crystal structure of Escherichia coli pyruvate kinase II

Crystal structure of Escherichia coli pyruvate kinase II

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)