3LM6 | pdb_00003lm6

Crystal Structure of Stage V sporulation protein AD (spoVAD) from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR525

PDB DOI: https://doi.org/10.2210/pdb3LM6/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-01-29 Released: 2010-02-16
Deposition Author(s): Forouhar, F., Su, M., Seetharaman, J., Fang, F., Xiao, R., Cunningham, K., Ma, L., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.241 (Depositor), 0.253 (DCC)
R-Value Work:
0.188 (Depositor), 0.202 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Northeast Structural Genomics Consortium Target SR525

Forouhar, F., Su, M., Seetharaman, J., Fang, F., Xiao, R., Cunningham, K., Ma, L., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 75.06 kDa
Atom Count: 5,021
Modeled Residue Count: 656
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stage V sporulation protein AD	A, B	346	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: BSU23410, spoVAD
UniProt
Find proteins for P40869 (Bacillus subtilis (strain 168)) Explore P40869 Go to UniProtKB: P40869
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40869
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.241 (Depositor), 0.253 (DCC)
R-Value Work: 0.188 (Depositor), 0.202 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.973	α = 90
b = 87.661	β = 90
c = 130.933	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-02-16

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Structure summary