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), 0.205 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YXY

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.205 (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

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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

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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.