1YHF | pdb_00001yhf

Crystal Structure of Conserved SPY1581 Protein of Unknown Function from Streptococcus pyogenes

PDB DOI: https://doi.org/10.2210/pdb1YHF/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Streptococcus pyogenes M1 GAS
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-01-07 Released: 2005-02-22
Deposition Author(s): Osipiuk, J., Lezondra, L., Moy, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.248 (Depositor), 0.209 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YHF

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

Literature

X-ray crystal structure of conserved hypothetical SPy1581 protein from Streptococcus pyogenes.

Osipiuk, J., Lezondra, L., Moy, S., Collart, F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 12.93 kDa
Atom Count: 981
Modeled Residue Count: 114
Deposited Residue Count: 115
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein SPy1581	A	115	Streptococcus pyogenes M1 GAS	Mutation(s): 6 Gene Names: SPy1581
UniProt
Find proteins for Q99YR1 (Streptococcus pyogenes serotype M1) Explore Q99YR1 Go to UniProtKB: Q99YR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99YR1
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: 2.00 Å
R-Value Free: 0.248 (Depositor), 0.209 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.897	α = 90
b = 39.897	β = 90
c = 144.758	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-02-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-02-22
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.