Macromolecule Content

Total Structure Weight: 162.46 kDa
Atom Count: 12,199
Modelled Residue Count: 1,423
Deposited Residue Count: 1,436
Unique protein chains: 1

5T1Q

2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Amidase from Staphylococcus aureus.

PDB DOI: https://doi.org/10.2210/pdb5T1Q/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-08-19 Released: 2017-06-07
Deposition Author(s): Minasov, G., Nocadello, S., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Bagnoli, F., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.219
R-Value Work: 0.173
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

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

Literature

2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Amidase from Staphylococcus aureus.

Minasov, G., Nocadello, S., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Bagnoli, F., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979	A, B, C, D	359	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0 Gene Names: SAOUHSC_02979
UniProt
Find proteins for Q2G222 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G222 Go to UniProtKB: Q2G222
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2G222
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C]	J [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D]	E [auth A], F [auth A], G [auth B], H [auth C], I [auth C], E [auth A], F [auth A], G [auth B], H [auth C], I [auth C], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.219
R-Value Work: 0.173
R-Value Observed: 0.175
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/m35t1q

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.57	α = 108.7
b = 66.838	β = 104.72
c = 102.737	γ = 90.25

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-06-07

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-06-07
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.