3LMA | pdb_00003lma

Crystal structure of the stage V sporulation protein AD (SpoVAD) from Bacillus licheniformis. Northeast Structural Genomics Consortium Target BiR6.

PDB DOI: https://doi.org/10.2210/pdb3LMA/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Bacillus licheniformis DSM 13 = ATCC 14580
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-01-29 Released: 2010-02-09
Deposition Author(s): Vorobiev, S., Ashok, S., Seetharaman, J., Belote, R.L., Ciccosanti, C., Patel, D.J., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.211 (Depositor), 0.209 (DCC)
R-Value Work:
0.168 (Depositor), 0.165 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of the stage V sporulation protein AD (SpoVAD) from Bacillus licheniformis.

Vorobiev, S., Ashok, S., Seetharaman, J., Belote, R.L., Ciccosanti, C., Patel, D.J., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 150.71 kDa
Atom Count: 9,962
Modelled Residue Count: 1,258
Deposited Residue Count: 1,388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stage V sporulation protein AD (SpoVAD)	A, B, C, D	347	Bacillus licheniformis DSM 13 = ATCC 14580	Mutation(s): 0 Gene Names: BL00782, BLi02491, spoVAD
UniProt
Find proteins for Q65HU8 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65HU8 Go to UniProtKB: Q65HU8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q65HU8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.211 (Depositor), 0.209 (DCC)
R-Value Work: 0.168 (Depositor), 0.165 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.957	α = 90
b = 83.059	β = 101.01
c = 103.662	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SHELXDE	phasing
SOLVE	phasing
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-02-09

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence
Version 1.3: 2018-01-24
Changes: Database references, Structure summary
Version 1.4: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.5: 2019-08-14
Changes: Data collection
Version 1.6: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary