1YXY | pdb_00001yxy

Crystal Structure of putative N-acetylmannosamine-6-P epimerase from Streptococcus pyogenes (APC29713) Structural genomics, MCSG

PDB DOI: https://doi.org/10.2210/pdb1YXY/pdb

Classification: ISOMERASE
Organism(s): Streptococcus pyogenes
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2005-02-22 Released: 2005-04-05
Deposition Author(s): Rotella, F.J., Zhang, R.G., Lezondra, L.E.O., Collart, F.R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.207 (Depositor), 0.200 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The 1.6 A crystal structure of putative N-acetylmannosamine-6-P epimerase from Streptococcus pyogenes

Rotella, F.J., Zhang, R.G., Lezondra, L.E.O., Collart, F.R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 50.19 kDa
Atom Count: 4,131
Modeled Residue Count: 460
Deposited Residue Count: 468
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative N-acetylmannosamine-6-phosphate 2-epimerase	A, B	234	Streptococcus pyogenes	Mutation(s): 0 Gene Names: nanE EC: 5.1.3.9
UniProt
Find proteins for P65522 (Streptococcus pyogenes serotype M1) Explore P65522 Go to UniProtKB: P65522
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P65522
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.207 (Depositor), 0.200 (DCC)
R-Value Work: 0.193 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.64	α = 90
b = 83.521	β = 90
c = 104.256	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-04-05

Deposition Author(s):

Lezondra, L.E.O.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-04-05
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references

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.