3MVN | pdb_00003mvn

Crystal structure of a domain from a putative UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-medo-diaminopimelate ligase from Haemophilus ducreyi 35000HP

PDB DOI: https://doi.org/10.2210/pdb3MVN/pdb

Classification: LIGASE
Organism(s): [Haemophilus] ducreyi 35000HP
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-05-04 Released: 2010-06-16
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, F.W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.237 (Depositor), 0.231 (DCC)
R-Value Work:
0.159 (Depositor), 0.163 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a domain from a putative UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-medo-diaminopimelate ligase from Haemophilus ducreyi 35000HP

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, F.W.

To be published.

Macromolecule Content

Total Structure Weight: 18.31 kDa
Atom Count: 1,027
Modelled Residue Count: 123
Deposited Residue Count: 163
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-medo-diaminopimelate ligase	A	163	[Haemophilus] ducreyi 35000HP	Mutation(s): 0 Gene Names: HD_0703, mpl EC: 6.3.2.45
UniProt
Find proteins for Q7VN73 (Haemophilus ducreyi (strain 35000HP / ATCC 700724)) Explore Q7VN73 Go to UniProtKB: Q7VN73
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7VN73
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.90 Å
R-Value Free: 0.237 (Depositor), 0.231 (DCC)
R-Value Work: 0.159 (Depositor), 0.163 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.996	α = 90
b = 46.996	β = 90
c = 106.628	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-06-16

Deposition Author(s):

Filippova, E.V.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-06-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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.