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- PDB-1a2j: OXIDIZED DSBA CRYSTAL FORM II -

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Basic information

Entry
Database: PDB / ID: 1a2j
TitleOXIDIZED DSBA CRYSTAL FORM II
ComponentsDISULFIDE BOND FORMATION PROTEIN
KeywordsOXIDOREDUCTASE / PROTEIN DISULFIDE ISOMERASE / PROTEIN FOLDING / REDOX PROTEIN / REDOX-ACTIVE CENTER
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space / periplasmic space / oxidoreductase activity
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 / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMartin, J.L. / Guddat, L.W.
Citation
Journal: Structure / Year: 1998
Title: Crystal structures of reduced and oxidized DsbA: investigation of domain motion and thiolate stabilization.
Authors: Guddat, L.W. / Bardwell, J.C. / Martin, J.L.
#1: Journal: Protein Sci. / Year: 1997
Title: The Uncharged Surface Features Surrounding the Active Site of Escherichia Coli Dsba are Conserved and are Implicated in Peptide Binding
Authors: Guddat, L.W. / Bardwell, J.C. / Zander, T. / Martin, J.L.
#2: Journal: Protein Sci. / Year: 1997
Title: Structural Analysis of Three His32 Mutants of Dsba: Support for an Electrostatic Role of His32 in Dsba Stability
Authors: Guddat, L.W. / Bardwell, J.C. / Glockshuber, R. / Huber-Wunderlich, M. / Zander, T. / Martin, J.L.
#3: Journal: Nature / Year: 1993
Title: Crystal Structure of the Dsba Protein Required for Disulphide Bond Formation in Vivo
Authors: Martin, J.L. / Bardwell, J.C. / Kuriyan, J.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of Dsba, an Escherichia Coli Protein Required for Disulphide Bond Formation in Vivo
Authors: Martin, J.L. / Waksman, G. / Bardwell, J.C. / Beckwith, J. / Kuriyan, J.
History
DepositionJan 6, 1998Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DISULFIDE BOND FORMATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,1551
Polymers21,1551
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.520, 51.380, 42.500
Angle α, β, γ (deg.)90.00, 103.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DISULFIDE BOND FORMATION PROTEIN / DSBA


Mass: 21155.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: PERIPLASM / References: UniProt: P24991, UniProt: P0AEG4*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.94 Å3/Da / Density % sol: 37 %
Crystal growpH: 5 / Details: 27% PEG 4K IN 0.1M ACETATE BUFFER PH 5.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
227 %PEG40001reservoir
30.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 10, 1995 / Details: YALE MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 38303 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 16
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 7.4 / Rsym value: 0.153 / % possible all: 81.6
Reflection
*PLUS
Num. obs: 10434 / Num. measured all: 38303
Reflection shell
*PLUS
% possible obs: 81.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FVK

1fvk


Resolution: 2→50 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 1
Details: EIGHT RESIDUES GLU 4, GLU 13, LYS 48, LYS 98, GLU 120, LYS 132, GLN 146, AND LYS 183 WERE MODELLED AS ALANINE BECAUSE OF POORLY DEFINED SIDE CHAIN DENSITY. RESIDUES GLU 85, SER 106, SER 133, ...Details: EIGHT RESIDUES GLU 4, GLU 13, LYS 48, LYS 98, GLU 120, LYS 132, GLN 146, AND LYS 183 WERE MODELLED AS ALANINE BECAUSE OF POORLY DEFINED SIDE CHAIN DENSITY. RESIDUES GLU 85, SER 106, SER 133, AND SER 186 WERE MODELLED WITH TWO ALTERNATE CONFORMATIONS, EACH OF HALF OCCUPANCY. THE SIDE CHAINS OF GLU 13, GLU 85, SER 106, SER 133, AND SER 186 WERE MODELLED WITH TWO ALTERNATE CONFORMATIONS, EACH OF HALF OCCUPANCY.
RfactorNum. reflection% reflection
Rfree0.227 1069 10 %
Rwork0.182 --
obs0.182 10332 93.3 %
Displacement parametersBiso mean: 23.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-50 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 0 90 1536
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.96
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.247 126 9.16 %
Rwork0.249 963 -
obs--79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.96

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