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- PDB-1fvj: THE 2.06 ANGSTROM STRUCTURE OF THE H32Y MUTANT OF THE DISULFIDE B... -

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Basic information

Entry
Database: PDB / ID: 1fvj
TitleTHE 2.06 ANGSTROM STRUCTURE OF THE H32Y MUTANT OF THE DISULFIDE BOND FORMATION PROTEIN (DSBA)
ComponentsDISULFIDE BOND FORMATION PROTEIN
KeywordsDISULFIDE OXIDOREDUCTASE / PROTEIN DISULFIDE ISOMERASE / PROTEIN FOLDING / REDOX PROTEIN DISULFIDE OXIDOREDUCTASE
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 / DIFFERENCE FOURIER / Resolution: 2.06 Å
AuthorsMartin, J.L. / Guddat, L.W.
Citation
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.
#1: 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.
#2: 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
DepositionAug 28, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 23, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,3602
Polymers42,3602
Non-polymers00
Water2,882160
1
A: DISULFIDE BOND FORMATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,1801
Polymers21,1801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DISULFIDE BOND FORMATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,1801
Polymers21,1801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.700, 65.100, 76.400
Angle α, β, γ (deg.)90.00, 126.30, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. EACH CONTAINS 189 RESIDUES, BUT THE LAST RESIDUE (189) IS NOT OBSERVED.

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Components

#1: Protein DISULFIDE BOND FORMATION PROTEIN / DSBA


Mass: 21180.053 Da / Num. of mol.: 2 / Mutation: H32Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P24991, UniProt: P0AEG4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Description: DATA WERE REJECTED AS FOLLOWS: FOR PAIRS WITH DIFFERENCE > 0.3*FHMEAN + 0.1FHSQ, THE PAIR WAS REJECTED IF DIFFERENCE > 3.0 TIMES ABOVE CRITERION.
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop / Details: Martin, J.L., (1993) J.Mol.Biol., 230, 1097.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-25 %(w/v)PEG80001reservoir
21 %MPD1reservoir
30.1 Mcacodylate1reservoir
41 %MPD1drop
520-25 %(w/v)PEG80001drop
60.1 Mcacodylate1drop
7DsbA solution1drop0.002ml

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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: Nov 5, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 26334 / % possible obs: 91 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.0558 / Net I/σ(I): 17.3
Reflection shellResolution: 2.06→2.25 Å / Redundancy: 1.98 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.89 / % possible all: 84.1
Reflection
*PLUS
Num. measured all: 74395
Reflection shell
*PLUS
% possible obs: 84.1 %

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Processing

Software
NameVersionClassification
R-AXISSOFTWAREdata collection
R-AXISSOFTWAREdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1DSB

1dsb


Resolution: 2.06→50 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.218 2607 10 %
Rwork0.18 --
obs0.18 26334 91 %
Displacement parametersBiso mean: 35.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.285 Å0.26 Å
Luzzati d res low-50 Å
Refinement stepCycle: LAST / Resolution: 2.06→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 0 164 3068
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.38
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.98
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.03
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: 2.06→2.15 Å
RfactorNum. reflection% reflection
Rfree0.297 291 8.05 %
Rwork0.283 2644 -
obs--81.2 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.98
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.03

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