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Yorodumi- PDB-1fvj: THE 2.06 ANGSTROM STRUCTURE OF THE H32Y MUTANT OF THE DISULFIDE B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fvj | ||||||
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Title | THE 2.06 ANGSTROM STRUCTURE OF THE H32Y MUTANT OF THE DISULFIDE BOND FORMATION PROTEIN (DSBA) | ||||||
Components | DISULFIDE BOND FORMATION PROTEIN | ||||||
Keywords | DISULFIDE 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.06 Å | ||||||
Authors | Martin, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fvj.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fvj.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fvj_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 1fvj_full_validation.pdf.gz | 431.8 KB | Display | |
Data in XML | 1fvj_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1fvj_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/1fvj ftp://data.pdbj.org/pub/pdb/validation_reports/fv/1fvj | HTTPS FTP |
-Related structure data
Related structure data | 1ac1C 1acvC 1fvkC 1dsbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. EACH CONTAINS 189 RESIDUES, BUT THE LAST RESIDUE (189) IS NOT OBSERVED. |
-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density 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. | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 5, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1DSB Resolution: 2.06→50 Å / σ(F): 1
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Displacement parameters | Biso mean: 35.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.06→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.15 Å
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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
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