2PY7

Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser complexed with ATP-Mg2+-Mn2+

PDB DOI: https://doi.org/10.2210/pdb2PY7/pdb

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

Deposited: 2007-05-15 Released: 2008-04-22
Deposition Author(s): Delbaere, L.T.J., Cotelesage, J.J.H., Goldie, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.218
R-Value Work: 0.155
R-Value Observed: 0.158

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser

Delbaere, L.T.J., Cotelesage, J.J.H., Goldie, H.

To be published.

Macromolecule Content

Total Structure Weight: 60.31 kDa
Atom Count: 4,737
Modelled Residue Count: 535
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase	A [auth X]	540	Escherichia coli K-12	Mutation(s): 1 Gene Names: pckA EC: 4.1.1.49
UniProt
Find proteins for P22259 (Escherichia coli (strain K12)) Explore P22259 Go to UniProtKB: P22259
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22259
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain E [auth X] MOL2 format, chain E [auth X]	E [auth X]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth X] Interactions & Density Focus chain E [auth X]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth X] SDF format, chain D [auth X] MOL2 format, chain C [auth X] MOL2 format, chain D [auth X]	C [auth X], D [auth X]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Focus chain D [auth X] Interactions & Density Focus chain C [auth X] Focus chain D [auth X]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X]	B [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.218
R-Value Work: 0.155
R-Value Observed: 0.158
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.999	α = 90
b = 95.663	β = 96.12
c = 46.319	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-04-22

Deposition Author(s):

Delbaere, L.T.J.

Cotelesage, J.J.H.

Goldie, H.

Revision History (Full details and data files)

Version 1.0: 2008-04-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description

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2PY7

Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser complexed with ATP-Mg2+-Mn2+

Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser

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)