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- PDB-3lma: Crystal structure of the stage V sporulation protein AD (SpoVAD) ... -

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Basic information

Entry
Database: PDB / ID: 3lma
TitleCrystal structure of the stage V sporulation protein AD (SpoVAD) from Bacillus licheniformis. Northeast Structural Genomics Consortium Target BiR6.
ComponentsStage V sporulation protein AD (SpoVAD)
KeywordsMEMBRANE PROTEIN / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Stage V sporulation protein AD / Stage V sporulation AD / Stage V sporulation AD superfamily / Stage V sporulation protein AD (SpoVAD) / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.993 Å
AuthorsVorobiev, S. / Ashok, S. / Seetharaman, J. / Belote, R.L. / Ciccosanti, C. / Patel, D.J. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. ...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)
CitationJournal: To be Published
Title: Crystal structure of the stage V sporulation protein AD (SpoVAD) from Bacillus licheniformis.
Authors: 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.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stage V sporulation protein AD (SpoVAD)
B: Stage V sporulation protein AD (SpoVAD)
C: Stage V sporulation protein AD (SpoVAD)
D: Stage V sporulation protein AD (SpoVAD)


Theoretical massNumber of molelcules
Total (without water)150,7054
Polymers150,7054
Non-polymers00
Water10,575587
1
A: Stage V sporulation protein AD (SpoVAD)
D: Stage V sporulation protein AD (SpoVAD)


Theoretical massNumber of molelcules
Total (without water)75,3532
Polymers75,3532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-31 kcal/mol
Surface area20470 Å2
MethodPISA
2
B: Stage V sporulation protein AD (SpoVAD)
C: Stage V sporulation protein AD (SpoVAD)


Theoretical massNumber of molelcules
Total (without water)75,3532
Polymers75,3532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-33 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.957, 83.059, 103.662
Angle α, β, γ (deg.)90.00, 101.01, 90.00
Int Tables number4
Space group name H-MP1211
Detailsdimmer according to aggregation screening

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Components

#1: Protein
Stage V sporulation protein AD (SpoVAD)


Mass: 37676.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: DSM 13 / ATCC 14580 / Gene: BL00782, BLi02491, spoVAD / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q65HU8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.47 %
Crystal growTemperature: 291 K / Method: icrobatch crystallization under paraffin oil / pH: 7.5
Details: 40% PEG 1000, 0.1M ammonium phosphate, 0.1M HEPES, pH 7.5, icrobatch crystallization under paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97916 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.993→50 Å / Num. all: 145826 / Num. obs: 142035 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 20.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 4.53 / Num. unique all: 14586 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
SHELXDEphasing
SOLVEphasing
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.993→38.939 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 3683 5.03 %RANDOM
Rwork0.1681 ---
obs0.1703 73163 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.18 Å2 / ksol: 0.32 e/Å3
Refinement stepCycle: LAST / Resolution: 1.993→38.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9375 0 0 587 9962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089524
X-RAY DIFFRACTIONf_angle_d1.37812881
X-RAY DIFFRACTIONf_dihedral_angle_d17.5653438
X-RAY DIFFRACTIONf_chiral_restr0.11508
X-RAY DIFFRACTIONf_plane_restr0.0051668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9928-2.0190.27081320.19292315X-RAY DIFFRACTION87
2.019-2.04660.22621430.1722659X-RAY DIFFRACTION99
2.0466-2.07590.23491280.16322698X-RAY DIFFRACTION99
2.0759-2.10690.231220.16972689X-RAY DIFFRACTION99
2.1069-2.13980.24281290.16332647X-RAY DIFFRACTION99
2.1398-2.17490.20851330.16572688X-RAY DIFFRACTION99
2.1749-2.21240.2241570.16922622X-RAY DIFFRACTION99
2.2124-2.25260.25571260.17072697X-RAY DIFFRACTION99
2.2526-2.29590.23311380.18342643X-RAY DIFFRACTION99
2.2959-2.34280.21761490.1652659X-RAY DIFFRACTION99
2.3428-2.39370.23471450.17512671X-RAY DIFFRACTION99
2.3937-2.44940.21871280.17882703X-RAY DIFFRACTION100
2.4494-2.51060.2561580.182696X-RAY DIFFRACTION100
2.5106-2.57850.2451450.17052658X-RAY DIFFRACTION100
2.5785-2.65430.20931370.16862702X-RAY DIFFRACTION100
2.6543-2.740.21981460.16992669X-RAY DIFFRACTION100
2.74-2.83790.23011460.17892727X-RAY DIFFRACTION100
2.8379-2.95150.2231500.1762707X-RAY DIFFRACTION100
2.9515-3.08580.22751220.18212725X-RAY DIFFRACTION100
3.0858-3.24840.23131480.16992693X-RAY DIFFRACTION100
3.2484-3.45180.19021480.16372674X-RAY DIFFRACTION100
3.4518-3.71810.18831650.15862684X-RAY DIFFRACTION100
3.7181-4.09190.17751610.1492696X-RAY DIFFRACTION100
4.0919-4.68320.16141480.13052689X-RAY DIFFRACTION99
4.6832-5.8970.16311360.15322746X-RAY DIFFRACTION100
5.897-38.94690.20941430.1782723X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.08280.04450.01830.01490.0464-0.0161-0.1229-0.2322-0.0276-0.0149-0.021-0.05750.0645-0.0938-0-0.1962-0.2865-0.0772-0.3634-0.1163-0.021220.198344.538940.2786
20.13690.0642-0.00770.00590.00420.0191-0.12120.0034-0.02370.07850.06420.09060.03520.12460-0.10610.0785-0.06860.0590.0407-0.0692
30.11480.00690.0384-0.00320.00770.0528-0.02830.0407-0.05540.0211-0.0070.00870.0321-0.0654-00.0522-0.00430.0234-0.02420.00890.0348
40.13410.08780.00760.03080.02180.0398-0.0304-0.05010.0157-0.0049-0.0114-0.02580.01580.0177-00.0599-0.0016-0.00620.0759-0.01620.0732
Refinement TLS groupSelection details: chain D

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