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- PDB-1su9: Reduced structure of the soluble domain of ResA -

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Basic information

Entry
Database: PDB / ID: 1su9
TitleReduced structure of the soluble domain of ResA
ComponentsThiol-disulfide oxidoreductase resA
KeywordsOXIDOREDUCTASE / Thioredoxin-like Domain / Alpha-Beta Protein / Soluble Domain / Membrane Protein
Function / homology
Function and homology information


cytochrome complex assembly / disulfide oxidoreductase activity / antioxidant activity / plasma membrane
Similarity search - Function
Thiol-disulphide oxidoreductase ResA / : / 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 ...Thiol-disulphide oxidoreductase ResA / : / 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
Thiol-disulfide oxidoreductase ResA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCrow, A. / Acheson, R.M. / Le Brun, N.E. / Oubrie, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Basis of Redox-coupled Protein Substrate Selection by the Cytochrome c Biosynthesis Protein ResA.
Authors: Crow, A. / Acheson, R.M. / Le Brun, N.E. / Oubrie, A.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol-disulfide oxidoreductase resA
B: Thiol-disulfide oxidoreductase resA


Theoretical massNumber of molelcules
Total (without water)31,8842
Polymers31,8842
Non-polymers00
Water5,405300
1
A: Thiol-disulfide oxidoreductase resA


Theoretical massNumber of molelcules
Total (without water)15,9421
Polymers15,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol-disulfide oxidoreductase resA


Theoretical massNumber of molelcules
Total (without water)15,9421
Polymers15,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.522, 59.653, 110.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological unit is a monomer of ResA

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Components

#1: Protein Thiol-disulfide oxidoreductase resA


Mass: 15942.131 Da / Num. of mol.: 2 / Fragment: Soluble Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: RESA, BSU23150 / Plasmid: pRAN11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P35160
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.4 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 27-32% PEG4000, 0.2M Ammonium Acetate, 0.1M Sodium Citrate pH 5.8, 40mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.95→26.2 Å / Num. all: 23398 / Num. obs: 23398 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 17 % / Rsym value: 0.089 / Net I/σ(I): 21
Reflection shellResolution: 1.95→2.02 Å / Mean I/σ(I) obs: 5.3 / Num. unique all: 2262 / Rsym value: 0.273 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Oxidised structure of ResA (PDB code: 1ST9) with all cysteines mutated to alanine.

1st9


Resolution: 1.95→26.2 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 1 / Stereochemistry target values: maximum likelihood
Details: 5% of the data was used for validation (ie as an 'Rfree') throughout, but upon completion of the model (Rfree=21.19, Rwork=18.31),an additional round of refinement using all data, including ...Details: 5% of the data was used for validation (ie as an 'Rfree') throughout, but upon completion of the model (Rfree=21.19, Rwork=18.31),an additional round of refinement using all data, including reflections marked as Rfree in the sf file, was performed to give a final crystallographic Rfactor (Rcryst=18.09).
RfactorNum. reflection% reflection
Rwork0.181 --
obs0.181 23330 99.6 %
all-23420 -
Refinement stepCycle: LAST / Resolution: 1.95→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 0 300 2457

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