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- PDB-2b3s: structure of the DSBA mutant (P31G-C33A) -

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Basic information

Entry
Database: PDB / ID: 2b3s
Titlestructure of the DSBA mutant (P31G-C33A)
ComponentsThiol:disulfide interchange protein dsbA
KeywordsOXIDOREDUCTASE / disulfide / thioredoxin / thiol-oxydase
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / 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 interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsVives, C. / Royant, A. / Serre, L.
CitationJournal: To be Published
Title: Structure of the DSBA mutant (P31G-C33A)
Authors: Vives, C. / Royant, A. / Serre, L.
History
DepositionSep 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 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 1.4Aug 23, 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

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbA
B: Thiol:disulfide interchange protein dsbA


Theoretical massNumber of molelcules
Total (without water)42,1662
Polymers42,1662
Non-polymers00
Water3,963220
1
A: Thiol:disulfide interchange protein dsbA


Theoretical massNumber of molelcules
Total (without water)21,0831
Polymers21,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Thiol:disulfide interchange protein dsbA


Theoretical massNumber of molelcules
Total (without water)21,0831
Polymers21,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-12 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.310, 56.310, 108.204
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Detailsbiological assembly consists in one monomer

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Components

#1: Protein Thiol:disulfide interchange protein dsbA / DsbA


Mass: 21082.896 Da / Num. of mol.: 2 / Fragment: enzyme DsbA / Mutation: P31G , C33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dsbA, dsf, ppfA / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEG4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.3 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9184
DetectorType: ADSC / Detector: CCD / Date: Nov 17, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.96→14.82 Å / Num. obs: 27226 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 36.9 Å2 / Rsym value: 0.057 / Net I/σ(I): 13
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.433 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.2refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U3A

1u3a


Resolution: 1.96→14.82 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.432 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25685 1418 5.2 %RANDOM
Rwork0.21372 ---
obs0.21598 25798 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.96→14.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 0 220 3158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223001
X-RAY DIFFRACTIONr_bond_other_d0.0010.022646
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9434056
X-RAY DIFFRACTIONr_angle_other_deg0.81136196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8755372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65825.833144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46715518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.966156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02590
X-RAY DIFFRACTIONr_nbd_refined0.2060.2691
X-RAY DIFFRACTIONr_nbd_other0.1720.22650
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21466
X-RAY DIFFRACTIONr_nbtor_other0.1090.21673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2040.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1441.52402
X-RAY DIFFRACTIONr_mcbond_other0.1681.5768
X-RAY DIFFRACTIONr_mcangle_it1.27622974
X-RAY DIFFRACTIONr_scbond_it1.75531366
X-RAY DIFFRACTIONr_scangle_it2.4894.51082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 109 -
Rwork0.29 1876 -
obs--98.41 %

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