2YXX | pdb_00002yxx

Crystal structure analysis of Diaminopimelate decarboxylate (lysA)

PDB DOI: https://doi.org/10.2210/pdb2YXX/pdb

Classification: LYASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-27 Released: 2007-10-30
Deposition Author(s): Nakamura, Y., Bessho, Y., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.220 (Depositor)
R-Value Work:
0.189 (Depositor)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2YXX

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure analysis of Diaminopimelate decarboxylate (lysA)

Nakamura, Y., Bessho, Y., Padmanabhan, B., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 44.81 kDa
Atom Count: 3,349
Modeled Residue Count: 385
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A	386	Thermotoga maritima MSB8	Mutation(s): 0 EC: 4.1.1.20
UniProt
Find proteins for Q9X1K5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1K5 Go to UniProtKB: Q9X1K5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X1K5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.220 (Depositor)
R-Value Work: 0.189 (Depositor)
R-Value Observed: 0.189 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.818	α = 90
b = 98.276	β = 90
c = 109.304	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-10-30

Deposition Author(s):

Padmanabhan, B.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-10-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.