2IA9

Structural Genomics, the crystal structure of SpoVG from Bacillus subtilis subsp. subtilis str. 168

PDB DOI: https://doi.org/10.2210/pdb2IA9/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2006-09-07 Released: 2006-10-17
Deposition Author(s): Tan, K., Borovilos, M., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.296 (Depositor), 0.290 (DCC)
R-Value Work:
0.227 (Depositor), 0.220 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The crystal structure of SpoVG from Bacillus subtilis subsp. subtilis str. 168

Tan, K., Borovilos, M., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 68.75 kDa
Atom Count: 4,499
Modelled Residue Count: 548
Deposited Residue Count: 600
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 septation protein spoVG	A, B, C, D, E A, B, C, D, E, F	100	Bacillus subtilis	Mutation(s): 3 Gene Names: spoVG, BSU00490
UniProt
Find proteins for P28015 (Bacillus subtilis (strain 168)) Explore P28015 Go to UniProtKB: P28015
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28015
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth D]	H [auth A], I [auth A], J [auth A], K [auth A], M [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain N [auth E] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth E] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth E]	G [auth A], L [auth B], N [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth E] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.296 (Depositor), 0.290 (DCC)
R-Value Work: 0.227 (Depositor), 0.220 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.464	α = 90
b = 136.464	β = 90
c = 110.493	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-10-17

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-10-17
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection
Version 1.5: 2024-11-20
Changes: Structure summary