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- PDB-3bd2: Crystal Structure of Staphylococcus aureus DsbA E96Q -

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Basic information

Entry
Database: PDB / ID: 3bd2
TitleCrystal Structure of Staphylococcus aureus DsbA E96Q
ComponentsDisulfide bond protein ADisulfide
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 formation protein D
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.81 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 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 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 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)21,8091
Polymers21,8091
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.418, 72.418, 92.684
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 / Disulfide / Thiol:disulfide oxidoreductase DsbA


Mass: 21808.994 Da / Num. of mol.: 1 / Fragment: residues in database 24-199 / Mutation: E96Q
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 / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 3.216901 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28-30% PEG 3350, VAPOR DIFFUSION, HANGING DROP, 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 19, 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: 1.81→36.21 Å / Num. all: 24212 / Num. obs: 24249 / % possible obs: 96 % / Observed criterion σ(F): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 31.4 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: 1033941.61 / Observed criterion F min: 0.89 / Rmerge(I) obs: 0.039 / Χ2: 1.423 / Net I/σ(I): 39.1
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2109 / Χ2: 2.137 / % possible all: 84.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
HKL-2000data reduction
PHASERphasing
RefinementStarting model: 3BCI

3bci


Resolution: 1.81→10 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2353 9.4 %random
Rwork0.243 ---
all-24956 --
obs-23690 94.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 52.947 Å2 / ksol: 0.291453 e/Å3
Displacement parametersBiso max: 71.6 Å2 / Biso mean: 32.256 Å2 / Biso min: 19.51 Å2
Baniso -1Baniso -2Baniso -3
1--3.799 Å2-2.724 Å20 Å2
2---3.799 Å20 Å2
3---7.598 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Luzzati d res high-1.81
Refinement stepCycle: LAST / Resolution: 1.81→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 0 225 1613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_torsion_deg21.7
X-RAY DIFFRACTIONc_torsion_impr_deg0.76
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 (%)
1.81-1.890.408244100.39922080.0263091245279.3
1.89-1.990.27230110.10.26926680.0163126296994.9
1.99-2.110.2593049.90.22927770.0153109308199.1
2.11-2.280.243308100.22727870.0143117309599.3
2.28-2.50.2613089.90.22427950.0153136310398.9
2.5-2.860.2452839.20.23127810.0153105306498.7
2.86-3.570.2422849.40.23927380.0143140302296.2
3.57-9.990.25432111.10.24825830.0143165290491.8
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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