3C5Q

Crystal structure of diaminopimelate decarboxylase (I148L mutant) from Helicobacter pylori complexed with L-lysine

PDB DOI: https://doi.org/10.2210/pdb3C5Q/pdb

Classification: LYASE
Organism(s): Helicobacter pylori
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-01 Released: 2008-05-27
Deposition Author(s): Hu, T., Wu, D., Jiang, H., Shen, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.253
R-Value Work: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of diaminopimelate decarboxylase from Helicobacter pylori

Hu, T., Wu, D., Ding, J., Jiang, H., Shen, X.

To be published.

Macromolecule Content

Total Structure Weight: 47.96 kDa
Atom Count: 3,254
Modelled Residue Count: 394
Deposited Residue Count: 425
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A	425	Helicobacter pylori	Mutation(s): 0 Gene Names: lysA EC: 4.1.1.20
UniProt
Find proteins for B4XMC6 (Helicobacter pylori) Explore B4XMC6 Go to UniProtKB: B4XMC6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4XMC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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]	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
LYS Query on LYS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.253
R-Value Work: 0.202
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.111	α = 90
b = 79.111	β = 90
c = 134.821	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-05-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources

3C5Q

Crystal structure of diaminopimelate decarboxylase (I148L mutant) from Helicobacter pylori complexed with L-lysine

Crystal structure of diaminopimelate decarboxylase from Helicobacter pylori

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)