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- PDB-3erw: Crystal Structure of StoA from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 3erw
TitleCrystal Structure of StoA from Bacillus subtilis
ComponentsSporulation thiol-disulfide oxidoreductase A
KeywordsOXIDOREDUCTASE / Thioredoxin-like fold / ResA-like fold / disulfide / dithiol / stoa / Redox-active center / Sporulation
Function / homology
Function and homology information


outer endospore membrane / sporulation resulting in formation of a cellular spore / antioxidant activity / cell redox homeostasis / oxidoreductase activity
Similarity search - Function
Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sporulation thiol-disulfide oxidoreductase A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsCrow, A. / Liu, Y. / Moller, M.C. / Le Brun, N.E. / Hederstedt, L.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure and Functional Properties of Bacillus subtilis Endospore Biogenesis Factor StoA
Authors: Crow, A. / Liu, Y. / Moller, M.C. / Le Brun, N.E. / Hederstedt, L.
History
DepositionOct 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sporulation thiol-disulfide oxidoreductase A
B: Sporulation thiol-disulfide oxidoreductase A
C: Sporulation thiol-disulfide oxidoreductase A
D: Sporulation thiol-disulfide oxidoreductase A
E: Sporulation thiol-disulfide oxidoreductase A
F: Sporulation thiol-disulfide oxidoreductase A
G: Sporulation thiol-disulfide oxidoreductase A


Theoretical massNumber of molelcules
Total (without water)115,4397
Polymers115,4397
Non-polymers00
Water1,76598
1
A: Sporulation thiol-disulfide oxidoreductase A


Theoretical massNumber of molelcules
Total (without water)16,4911
Polymers16,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sporulation thiol-disulfide oxidoreductase A


Theoretical massNumber of molelcules
Total (without water)16,4911
Polymers16,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sporulation thiol-disulfide oxidoreductase A


Theoretical massNumber of molelcules
Total (without water)16,4911
Polymers16,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sporulation thiol-disulfide oxidoreductase A


Theoretical massNumber of molelcules
Total (without water)16,4911
Polymers16,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Sporulation thiol-disulfide oxidoreductase A


Theoretical massNumber of molelcules
Total (without water)16,4911
Polymers16,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Sporulation thiol-disulfide oxidoreductase A


Theoretical massNumber of molelcules
Total (without water)16,4911
Polymers16,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Sporulation thiol-disulfide oxidoreductase A


Theoretical massNumber of molelcules
Total (without water)16,4911
Polymers16,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.717, 133.717, 64.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 31:164 )
211chain B and (resseq 31:164 )
311chain C and (resseq 35:164 )
411chain D and (resseq 31:164 )
511chain E and (resseq 31:164 )
611chain F and (resseq 34:164 )
711chain G and (resseq 32:164 )

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Components

#1: Protein
Sporulation thiol-disulfide oxidoreductase A / Stage IV sporulation protein H


Mass: 16491.352 Da / Num. of mol.: 7 / Fragment: UNP residues 22 to 164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 1a1 / Gene: BSU13840, spoIVH, stoA / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: O31687
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 27% PEG 2000, 0.2 M Ammonium acetate, 0.1 M sodium acetate pH 4.8. Cryoprotected with 20 % ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorDetector: CCD / Date: Dec 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→36.27 Å / Num. obs: 44319 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rsym value: 0.083 / Net I/σ(I): 16.1
Reflection shellResolution: 2.5→2.64 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 6023 / Rsym value: 0.293 / % possible all: 83.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BP3model building
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
BP3phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→36.274 Å / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: TWIN_LSQ_F
Details: Twin refinement twinning fraction 0.36 twinning operator -k,-h-l
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 4415 5.02 %RANDOM
Rwork0.1828 ---
obs0.1838 44319 97.99 %-
all-44319 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.266 Å2 / ksol: 0.349 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→36.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7640 0 0 98 7738
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1095X-RAY DIFFRACTIONPOSITIONAL
12B1095X-RAY DIFFRACTIONPOSITIONAL0.032
13C1060X-RAY DIFFRACTIONPOSITIONAL0.04
14D1095X-RAY DIFFRACTIONPOSITIONAL0.031
15E1086X-RAY DIFFRACTIONPOSITIONAL0.034
16F1067X-RAY DIFFRACTIONPOSITIONAL0.033
17G1088X-RAY DIFFRACTIONPOSITIONAL0.035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.54320.2652000.22663464X-RAY DIFFRACTION98
2.5432-2.58950.25811480.21433868X-RAY DIFFRACTION98
2.5895-2.63930.24861940.22083983X-RAY DIFFRACTION98
2.6393-2.69310.22312170.21484218X-RAY DIFFRACTION98
2.6931-2.75170.2252050.21824254X-RAY DIFFRACTION98
2.7517-2.81560.23532480.20314184X-RAY DIFFRACTION98
2.8156-2.8860.21132680.19074202X-RAY DIFFRACTION98
2.886-2.9640.23642340.1994326X-RAY DIFFRACTION98
2.964-3.05120.19842340.19194228X-RAY DIFFRACTION98
3.0512-3.14960.22462500.19534150X-RAY DIFFRACTION98
3.1496-3.26210.19572320.18484328X-RAY DIFFRACTION98
3.2621-3.39270.19222260.1764290X-RAY DIFFRACTION98
3.3927-3.54690.18642320.16974170X-RAY DIFFRACTION98
3.5469-3.73380.18772180.16064281X-RAY DIFFRACTION98
3.7338-3.96740.16722300.1554229X-RAY DIFFRACTION98
3.9674-4.27330.16221900.15274318X-RAY DIFFRACTION98
4.2733-4.70250.15972050.14824253X-RAY DIFFRACTION98
4.7025-5.38110.17332240.16494296X-RAY DIFFRACTION98
5.3811-6.77240.24242500.22184202X-RAY DIFFRACTION98
6.7724-36.27770.25261870.21054252X-RAY DIFFRACTION98

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