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- PDB-4ocf: Crystal structure of the disulfide oxidoreductase DsbA (S30XXC33)... -

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Basic information

Entry
Database: PDB / ID: 4ocf
TitleCrystal structure of the disulfide oxidoreductase DsbA (S30XXC33) active site mutant from Proteus mirabilis
ComponentsThiol:disulfide interchange protein
KeywordsOXIDOREDUCTASE / Oxidative folding protein / virulence factor maturation protein / disulfide oxidoreductase / Thioredoxin / DsbA / Dithiol exchange / DsbB / Periplasmic
Function / homology
Function and homology information


disulfide oxidoreductase activity / 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
THIOCYANATE ION / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 Å
AuthorsKurth, F. / Martin, J.L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure of the Dithiol Oxidase DsbA Enzyme from Proteus Mirabilis Bound Non-covalently to an Active Site Peptide Ligand.
Authors: Kurth, F. / Duprez, W. / Premkumar, L. / Schembri, M.A. / Fairlie, D.P. / Martin, J.L.
History
DepositionJan 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein
B: Thiol:disulfide interchange protein
C: Thiol:disulfide interchange protein
D: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,56913
Polymers84,0474
Non-polymers5239
Water14,592810
1
A: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1864
Polymers21,0121
Non-polymers1743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2445
Polymers21,0121
Non-polymers2324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0702
Polymers21,0121
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0702
Polymers21,0121
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.990, 80.210, 114.450
Angle α, β, γ (deg.)90.00, 91.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thiol:disulfide interchange protein


Mass: 21011.627 Da / Num. of mol.: 4 / Mutation: C30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: HI4320 / Gene: dsbA, PMI2828 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: B4EZ68
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: KSCN, PEG33500, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2012
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.979→57.22 Å / Num. all: 47865 / Num. obs: 47865 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 12.34 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3
Reflection shellResolution: 1.979→2.09 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 8.4 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OCE

4oce


Resolution: 1.979→57.215 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 2011 4.2 %
Rwork0.1524 --
obs0.155 47837 99.67 %
all-47837 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.979→57.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5833 0 27 810 6670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115976
X-RAY DIFFRACTIONf_angle_d1.2448081
X-RAY DIFFRACTIONf_dihedral_angle_d14.6912190
X-RAY DIFFRACTIONf_chiral_restr0.072898
X-RAY DIFFRACTIONf_plane_restr0.0071055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9788-2.02830.24091430.15193198X-RAY DIFFRACTION98
2.0283-2.08320.25021380.15073263X-RAY DIFFRACTION100
2.0832-2.14450.24141430.15013241X-RAY DIFFRACTION100
2.1445-2.21370.20351390.14793297X-RAY DIFFRACTION100
2.2137-2.29280.26131460.15833246X-RAY DIFFRACTION100
2.2928-2.38460.23631440.15373296X-RAY DIFFRACTION100
2.3846-2.49320.23611460.15963224X-RAY DIFFRACTION100
2.4932-2.62460.21831450.15753264X-RAY DIFFRACTION100
2.6246-2.7890.24441430.1683275X-RAY DIFFRACTION100
2.789-3.00440.24391440.17053268X-RAY DIFFRACTION100
3.0044-3.30670.23611430.16923289X-RAY DIFFRACTION100
3.3067-3.78510.16961460.14283326X-RAY DIFFRACTION100
3.7851-4.76850.15941420.12643292X-RAY DIFFRACTION100
4.7685-57.23910.1641490.14893347X-RAY DIFFRACTION100

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