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- PDB-3bci: Crystal Structure of Staphylococcus aureus DsbA -

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Basic information

Entry
Database: PDB / ID: 3bci
TitleCrystal Structure of Staphylococcus aureus DsbA
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 / SYNCHROTRON / MAD / Resolution: 1.81 Å
AuthorsHeras, B. / Thony-Meyer, L. / Martin, J.L.
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Expression and crystallization of DsbA from Staphylococcus aureus
Authors: Heras, B. / Kurz, M. / Jarrott, R. / Byriel, K.A. / Jones, A. / Thony-Meyer, L. / Martin, J.L.
History
DepositionNov 12, 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 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)21,8101
Polymers21,8101
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.099, 72.099, 92.098
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 21809.979 Da / Num. of mol.: 1 / Fragment: residues in database 24-199
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.: 231 / 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: 3.168319 Å3/Da / Density % sol: 65.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 28-30% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT11.54
SYNCHROTRONALS 8.3.120.9796, 0.9797, 0.95373
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEDec 16, 2004Osmic Confocal Max-Flux optics
ADSC QUANTUM 2102CCDJun 9, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Osmic Confocal MaxFluxSINGLE WAVELENGTHMx-ray1
2Double flat crystal, Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.97961
30.97971
40.953731
ReflectionRedundancy: 8.2 % / Av σ(I) over netI: 10.5 / Number: 156671 / Rmerge(I) obs: 0.088 / Χ2: 0.87 / D res high: 1.99 Å / D res low: 50 Å / Num. obs: 19033 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.295099.910.0591.68.3
3.44.2910010.0631.4068.5
2.973.410010.0771.0378.5
2.72.9710010.0970.8988.6
2.512.710010.1190.7058.5
2.362.5110010.1430.6798.5
2.242.3610010.1730.6328.5
2.142.2410010.2050.588.5
2.062.1410010.2490.5517.8
1.992.0699.710.3150.5036.5
ReflectionResolution: 1.8→37.06 Å / Num. all: 24921 / Num. obs: 24921 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 25.1 Å2 / Limit h max: 34 / Limit h min: 0 / Limit k max: 34 / Limit k min: 0 / Limit l max: 50 / Limit l min: 0 / Observed criterion F max: 460920.71 / Observed criterion F min: 2.97 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2272 / % possible all: 91.6

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Processing

Software
NameVersionClassificationNB
d*TREK9.1SSIdata scaling
CNS1.1refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
d*TREKdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.81→29.57 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.2 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2432 9.8 %random
Rwork0.198 ---
all-24756 --
obs-24569 99.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 48.282 Å2 / ksol: 0.313641 e/Å3
Displacement parametersBiso max: 85.88 Å2 / Biso mean: 35.14 Å2 / Biso min: 16.26 Å2
Baniso -1Baniso -2Baniso -3
1--3.827 Å2-2.399 Å20 Å2
2---3.827 Å20 Å2
3---7.654 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.36 Å
Luzzati d res high-1.81
Refinement stepCycle: LAST / Resolution: 1.81→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 0 231 1624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg20.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.7
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.81-1.890.4042889.90.38426090.0243089289793.8
1.89-1.990.3313009.70.30727780.0193082307899.8
1.99-2.120.282919.40.2427960.0163091308799.9
2.12-2.280.22431310.20.18327690.0133083308299.9
2.28-2.510.216308100.18927790.0123089308799.9
2.51-2.870.23132010.30.18727820.01331023102100
2.87-3.620.2113089.90.18527910.01230993099100
3.62-29.570.173049.70.16828330.0131373137100
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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