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- PDB-1fvk: THE 1.7 ANGSTROM STRUCTURE OF WILD TYPE DISULFIDE BOND FORMATION ... -

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Basic information

Entry
Database: PDB / ID: 1fvk
TitleTHE 1.7 ANGSTROM STRUCTURE OF WILD TYPE DISULFIDE BOND FORMATION PROTEIN (DSBA)
ComponentsDISULFIDE BOND FORMATION PROTEIN
KeywordsDISULFIDE OXIDOREDUCTASE / 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 / MIR / Resolution: 1.7 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 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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
Remark 650HELIX HELIX A1' IS SEPARATED FROM A1 BY A THREE RESIDUE LOOP. HELIX B1' IS SEPARATED FROM B1 BY A ...HELIX HELIX A1' IS SEPARATED FROM A1 BY A THREE RESIDUE LOOP. HELIX B1' IS SEPARATED FROM B1 BY A THREE RESIDUE LOOP. HELIX A3 IS KINKED BY PRO A 91 AND HELIX B3 BY PRO B 91.

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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
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
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. THE ACTIVE SITE DISULFIDE RESIDUES ARE CYS 30 AND CYS 33. PRO 151 FORMS PART OF THE ACTIVE SITE.

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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 natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P24991, UniProt: P0AEG4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growpH: 7.5 / Details: pH 7.5

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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: Jul 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: 1.7→50 Å / Num. obs: 46502 / % possible obs: 90.5 % / Observed criterion σ(I): 0.3 / Redundancy: 2.8 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.0635 / Net I/σ(I): 14.1
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.36 / % possible all: 84.1

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Processing

Software
NameVersionClassification
RIGAKUSOFTWAREdata collection
RIGAKUSOFTWAREdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
RIGAKUdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1DSD

1dsd


Resolution: 1.7→50 Å / Cross valid method: YES / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4483 10 %YES
Rwork0.198 ---
obs0.198 46502 90.5 %-
Displacement parametersBiso mean: 33.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.275 Å0.22 Å
Luzzati d res low-50 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 0 248 3147
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.39
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.86
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.06
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: 1.7→1.78 Å
RfactorNum. reflection% reflection
Rfree0.4 545 8.51 %
Rwork0.398 4478 -
obs--78.3 %

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