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- PDB-6bs9: Stage III sporulation protein AB (SpoIIIAB) -

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Basic information

Entry
Database: PDB / ID: 6bs9
TitleStage III sporulation protein AB (SpoIIIAB)
ComponentsStage III sporulation protein AB
KeywordsTRANSPORT PROTEIN / Secretion system / Sporulation
Function / homologyStage III sporulation protein AB / Stage III sporulation protein AB (spore_III_AB) / sporulation resulting in formation of a cellular spore / Stage III sporulation protein AB
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.32 Å
AuthorsStrynadka, N.C.J. / Zeytuni, N. / Camp, A.H. / Flanagan, K.A.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structural characterization of SpoIIIAB sporulation-essential protein in Bacillus subtilis.
Authors: Zeytuni, N. / Flanagan, K.A. / Worrall, L.J. / Massoni, S.C. / Camp, A.H. / Strynadka, N.C.J.
History
DepositionDec 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stage III sporulation protein AB
B: Stage III sporulation protein AB
C: Stage III sporulation protein AB
D: Stage III sporulation protein AB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,29412
Polymers58,5264
Non-polymers7698
Water2,054114
1
A: Stage III sporulation protein AB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9204
Polymers14,6311
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Stage III sporulation protein AB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8243
Polymers14,6311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Stage III sporulation protein AB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7272
Polymers14,6311
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Stage III sporulation protein AB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8243
Polymers14,6311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.540, 82.000, 84.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-337-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLNGLNAA23 - 1481 - 126
21GLYGLYGLNGLNBB23 - 1481 - 126
12METMETALAALAAA26 - 1474 - 125
22METMETALAALACC26 - 1474 - 125
13GLYGLYGLNGLNAA23 - 1481 - 126
23GLYGLYGLNGLNDD23 - 1481 - 126
14METMETALAALABB26 - 1474 - 125
24METMETALAALACC26 - 1474 - 125
15GLYGLYALAALABB23 - 1491 - 127
25GLYGLYALAALADD23 - 1491 - 127
16METMETALAALACC26 - 1474 - 125
26METMETALAALADD26 - 1474 - 125

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Stage III sporulation protein AB


Mass: 14631.416 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: spoIIIAB, BSU24420 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q01368
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.15 M potassium phosphate and 3.3 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.32→82 Å / Num. obs: 23068 / % possible obs: 99.9 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.037 / Rrim(I) all: 0.136 / Χ2: 1.445 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.32-2.367.30.60211100.7470.2210.6440.86598.1
2.36-2.49.10.74611420.8240.2480.7880.86499.6
2.4-2.4510.60.66311150.9020.2050.6950.90999.9
2.45-2.511.90.69111520.9010.2040.7210.924100
2.5-2.5512.90.62611140.9210.1770.6510.913100
2.55-2.6113.60.5611340.9370.1560.5820.919100
2.61-2.6814.10.50811500.9480.1390.5270.997100
2.68-2.7514.30.46511350.9530.1270.4820.996100
2.75-2.8314.30.36811400.9710.10.3821.063100
2.83-2.9214.30.28411430.9840.0770.2941.114100
2.92-3.0314.40.24311490.9890.0660.2521.233100
3.03-3.1514.40.20211430.9910.0550.2091.283100
3.15-3.2914.30.16711530.9950.0460.1731.423100
3.29-3.4714.30.14911440.9960.0410.1541.552100
3.47-3.68130.13911680.9950.040.1452.349100
3.68-3.9713.20.10911490.9970.0310.1142.722100
3.97-4.3714.10.07911710.9980.0220.0821.961100
4.37-514.20.06711850.9980.0180.071.907100
5-6.29140.07611970.9990.0210.0791.576100
6.29-5012.60.06312740.9990.0180.0652.61899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→82 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 17.803 / SU ML: 0.207 / SU R Cruickshank DPI: 0.4357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.436 / ESU R Free: 0.266
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 1072 4.7 %RANDOM
Rwork0.2069 ---
obs0.2093 21942 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.63 Å2 / Biso mean: 46.069 Å2 / Biso min: 26.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å2-0 Å2
2---2.93 Å20 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 2.32→82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4009 0 40 114 4163
Biso mean--68.68 42.96 -
Num. residues----507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194120
X-RAY DIFFRACTIONr_bond_other_d0.0120.023958
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9545548
X-RAY DIFFRACTIONr_angle_other_deg2.01239134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7495505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.68425.206194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27515780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.431521
X-RAY DIFFRACTIONr_chiral_restr0.1040.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024604
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02923
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A148520.11
12B148520.11
21A140540.12
22C140540.12
31A142000.14
32D142000.14
41B140120.13
42C140120.13
51B141800.14
52D141800.14
61C144500.11
62D144500.11
LS refinement shellResolution: 2.321→2.381 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 66 -
Rwork0.268 1543 -
all-1609 -
obs--96.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.2703-0.1153-0.44051.69610.01730.74070.0098-0.07030.023-0.05680.0205-0.0369-0.0110.0906-0.03020.02840.01160.01020.1335-0.02020.008519.264-18.5821-2.1379
20.32410.0065-0.50780.75310.09620.8249-0.0025-0.08110.0080.04490.02650.0496-0.00080.1718-0.02390.02320.01710.01460.1474-0.02240.018837.497-22.944-23.2564
31.36940.0453-0.56061.94310.12330.249-0.03650.0820.0475-0.10090.0662-0.02810.0087-0.0611-0.02970.0191-0.01330.00560.1220.02350.00984.0456-26.3232-16.4852
40.121-0.1949-0.19531.2288-0.37481.2513-0.0050.0851-0.00860.06110.03930.0798-0.0455-0.104-0.03440.033-0.00510.02210.1570.00640.016621.2852-14.8851-36.2999
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 152
2X-RAY DIFFRACTION2B23 - 149
3X-RAY DIFFRACTION3C26 - 148
4X-RAY DIFFRACTION4D23 - 149

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