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- PDB-4oce: Crystal structure of the disulfide oxidoreductase DsbA from Prote... -

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Basic information

Entry
Database: PDB / ID: 4oce
TitleCrystal structure of the disulfide oxidoreductase DsbA from Proteus mirabilis
ComponentsThiol:disulfide interchange protein
KeywordsOXIDOREDUCTASE / Oxidative folding protein / virulence factor maturation protein / disulfide oxidoreductase / Thioredoxin fold / 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
MALONATE ION / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesProteus mirabilis HI4320 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.768 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1302
Polymers21,0281
Non-polymers1021
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.830, 37.830, 298.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-420-

HOH

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Components

#1: Protein Thiol:disulfide interchange protein


Mass: 21027.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis HI4320 (bacteria) / Strain: HI4320 / Gene: dsbA, PMI2828 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: B4EZ68
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG3350, Sodium Malonate, pH 5.0, 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: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2011
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.768→42.64 Å / Num. all: 22817 / Num. obs: 22817 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 16.1
Reflection shellResolution: 1.768→1.86 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3207 / % possible all: 100

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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: 1DSB

1dsb


Resolution: 1.768→37.53 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 13.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.169 1159 5.11 %Random
Rwork0.1476 ---
all0.1487 22686 --
obs0.1487 22686 100 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.768→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 7 268 1743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091531
X-RAY DIFFRACTIONf_angle_d1.1522078
X-RAY DIFFRACTIONf_dihedral_angle_d14.174566
X-RAY DIFFRACTIONf_chiral_restr0.065229
X-RAY DIFFRACTIONf_plane_restr0.006277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.768-1.84850.2191290.17292615X-RAY DIFFRACTION100
1.8485-1.9460.19221340.14852604X-RAY DIFFRACTION100
1.946-2.06790.18911390.14322651X-RAY DIFFRACTION100
2.0679-2.22750.1641610.13192644X-RAY DIFFRACTION100
2.2275-2.45160.17741540.13332601X-RAY DIFFRACTION100
2.4516-2.80630.16291510.1422684X-RAY DIFFRACTION100
2.8063-3.53520.15221330.14782763X-RAY DIFFRACTION100
3.5352-37.53810.16161580.1592965X-RAY DIFFRACTION100

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