9EVF | pdb_00009evf

Citramalate lyase - ADP - pyruvate complex

PDB DOI: https://doi.org/10.2210/pdb9EVF/pdb

Classification: LYASE
Organism(s): Klebsiella planticola
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-03-29 Released: 2025-10-08
Deposition Author(s): Ermler, U., Berg, I., Demmer, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.195 (Depositor), 0.195 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9EVF

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Novel citramalate lyase involved in glutamate fermentation of enterobacteria

Eggers, J., Schaefer, L., Cassens, E.A., Schmid, L., Simon, S.A., Probst, A.J., Koenig, S., Demmer, U., Ermler, U., Berg, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 123.86 kDa
Atom Count: 9,725
Modeled Residue Count: 1,122
Deposited Residue Count: 1,122
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citramalate lyase, subunit A (cmlA)	A, C	456	Klebsiella planticola	Mutation(s): 0
UniProt
Find proteins for A0A0P8H7C5 (Citrobacter freundii) Explore A0A0P8H7C5 Go to UniProtKB: A0A0P8H7C5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0P8H7C5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Citramalate lyase, subunit B (cmlB)	B, D	105	Klebsiella planticola	Mutation(s): 0
UniProt
Find proteins for A0A564JVI2 (Klebsiella spallanzanii) Explore A0A564JVI2 Go to UniProtKB: A0A564JVI2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A564JVI2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C]	E [auth A], L [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth C]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain I [auth A]	I [auth A], J [auth A], P [auth C], Q [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth C] Focus chain Q [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth C] Focus chain Q [auth D]
PYR (Subject of Investigation/LOI) Query on PYR Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth C] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] mmCIF format, chain H [auth A] mmCIF format, chain O [auth C]	H [auth A], O [auth C]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth C] Interactions & Density Focus chain H [auth A] Focus chain O [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain N [auth C] SDF format, chain M [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C]	F [auth A], G [auth A], M [auth C], N [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.195 (Depositor), 0.195 (DCC)
R-Value Work: 0.178 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.21	α = 90
b = 108.34	β = 90
c = 98.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

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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.