2EK0 | pdb_00002ek0

Stage V Sporolation Protein S (SPOVS) from Thermus thermophilus Zinc form

PDB DOI: https://doi.org/10.2210/pdb2EK0/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Thermus thermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-03-22 Released: 2007-09-25
Deposition Author(s): Rehse, P.H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.255 (Depositor), 0.246 (DCC)
R-Value Work:
0.229 (Depositor), 0.224 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Stage V Sporolation Protein S (SPOVS) from Thermus thermophilus Zinc form

Rehse, P.H., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 19.59 kDa
Atom Count: 1,421
Modeled Residue Count: 180
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stage V sporulation protein S (SpoVS) related protein	A, B	90	Thermus thermophilus	Mutation(s): 1 Gene Names: HB8
UniProt
Find proteins for Q5SK02 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SK02 Go to UniProtKB: Q5SK02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SK02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.255 (Depositor), 0.246 (DCC)
R-Value Work: 0.229 (Depositor), 0.224 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.237	α = 90
b = 72.772	β = 90
c = 68.438	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-25

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-09-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-10-25
Changes: Data collection, Refinement description

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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.