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- PDB-1a2m: OXIDIZED DSBA AT 2.7 ANGSTROMS RESOLUTION, CRYSTAL FORM III -

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Basic information

Entry
Database: PDB / ID: 1a2m
TitleOXIDIZED DSBA AT 2.7 ANGSTROMS RESOLUTION, CRYSTAL FORM III
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 ...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: 2.7 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: 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.
#2: 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.
#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 1.0Jul 8, 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
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DISULFIDE BOND FORMATION PROTEIN
B: DISULFIDE BOND FORMATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)42,3102
Polymers42,3102
Non-polymers00
Water45025
1
A: DISULFIDE BOND FORMATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,1551
Polymers21,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DISULFIDE BOND FORMATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,1551
Polymers21,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.380, 83.800, 58.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DISULFIDE BOND FORMATION PROTEIN / DSBA


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


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 49 %
Crystal growpH: 5.6
Details: 0.2 M AMMONIUM ACETATE, 0.1M SODIUM CITRATE PH 5.6 30% (W/V) PEG 4000.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop / Details: Martin, J.L., (1993) J.Mol.Biol., 230, 1097.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-25 %(w/v)PEG80001reservoir
21 %MPD1reservoir
30.1 Mcacodylate1reservoir
40.5 %MPD1drop
510-12.5 %(w/v)PEG80001drop
60.05 Mcacodylate1drop
711 mg/mlDsbA1drop

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 10, 1996 / Details: YALE MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18501 / % possible obs: 73.6 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.294 / % possible all: 56.1
Reflection
*PLUS
Num. obs: 10864 / % possible obs: 86.1 % / Num. measured all: 43081 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 69.9 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FVK

1fvk


Resolution: 2.7→50 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.308 1103 10 %
Rwork0.261 --
obs0.261 10710 83.5 %
Displacement parametersBiso mean: 24.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-50 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 0 25 2780
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
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_deg0.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.89
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: 2.7→2.8 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.411 98 6.4 %
Rwork0.319 813 -
obs--59 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.89

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