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- PDB-3bck: Crystal Structure of Staphylococcus aureus DsbA T153V -

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Basic information

Entry
Database: PDB / ID: 3bck
TitleCrystal Structure of Staphylococcus aureus DsbA T153V
ComponentsDisulfide bond protein A
KeywordsOXIDOREDUCTASE / thiol-disulfide oxidoreductase / redox protein / protein folding / redox active centre
Function / homology
Function and homology information


Thioredoxin / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disulfide bond protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHeras, B. / Thony-Meyer, L. / Martin, J.L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Staphylococcus aureus DsbA Does Not Have a Destabilizing Disulfide: A NEW PARADIGM FOR BACTERIAL OXIDATIVE FOLDING
Authors: Heras, B. / Kurz, M. / Jarrott, R. / Shouldice, S.R. / Frei, P. / Robin, G. / Cemazar, M. / Thony-Meyer, L. / Glockshuber, R. / Martin, J.L.
History
DepositionNov 13, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disulfide bond protein A


Theoretical massNumber of molelcules
Total (without water)21,8081
Polymers21,8081
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.085, 72.085, 92.575
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Disulfide bond protein A / Thiol:disulfide oxidoreductase DsbA


Mass: 21808.006 Da / Num. of mol.: 1 / Fragment: residues in database 24-199 / Mutation: T153V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: BB270 / Gene: AAG41993 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: Q9EYL5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.18378 Å3/Da / Density % sol: 65.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 28-30% PEG 3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 3, 2006 / Details: Osmic Confocal Max-Flux optics
RadiationMonochromator: Osmic Confocal MaxFlux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→62.43 Å / Num. all: 19271 / Num. obs: 19271 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Redundancy: 5.06 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.07 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1817 / % possible all: 92

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BCI

3bci


Resolution: 1.95→62.43 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 910 -RANDOM
Rwork0.223 ---
all-19903 --
obs-19156 96.1 %-
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.3 Å22.08 Å20 Å2
2--7.3 Å20 Å2
3----14.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 1.95→62.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 0 154 1540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.035
RfactorNum. reflection% reflection
Rfree0.437 141 -
Rwork0.412 --
obs-2880 91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water.param

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