3HP7 | pdb_00003hp7

Putative hemolysin from Streptococcus thermophilus.

PDB DOI: https://doi.org/10.2210/pdb3HP7/pdb

Classification: structural genomics, unknown function
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-06-03 Released: 2009-06-16
Deposition Author(s): Osipiuk, J., Hatzos, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.177 (Depositor), 0.185 (DCC)
R-Value Work:
0.145 (Depositor), 0.154 (DCC)
R-Value Observed:
0.147 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3HP7

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

Literature

X-ray crystal structure of putative hemolysin from Streptococcus thermophilus.

Osipiuk, J., Hatzos, C., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 32.47 kDa
Atom Count: 2,687
Modeled Residue Count: 275
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin, putative	A	291	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: stu1215
UniProt
Find proteins for Q5M3Z4 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M3Z4 Go to UniProtKB: Q5M3Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5M3Z4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.53 Å
R-Value Free: 0.177 (Depositor), 0.185 (DCC)
R-Value Work: 0.145 (Depositor), 0.154 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.958	α = 90
b = 81.713	β = 90
c = 95.537	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-16

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-06-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-10-16
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.