[English] 日本語
Yorodumi- PDB-1fvk: THE 1.7 ANGSTROM STRUCTURE OF WILD TYPE DISULFIDE BOND FORMATION ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fvk | ||||||
---|---|---|---|---|---|---|---|
Title | THE 1.7 ANGSTROM STRUCTURE OF WILD TYPE DISULFIDE BOND FORMATION PROTEIN (DSBA) | ||||||
Components | DISULFIDE BOND FORMATION PROTEIN | ||||||
Keywords | DISULFIDE 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.7 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 |
| ||||||
Remark 650 | HELIX 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fvk.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fvk.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fvk_validation.pdf.gz | 433.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1fvk_full_validation.pdf.gz | 435.5 KB | Display | |
Data in XML | 1fvk_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 1fvk_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/1fvk ftp://data.pdbj.org/pub/pdb/validation_reports/fv/1fvk | HTTPS FTP |
-Related structure data
Related structure data | 1ac1C 1acvC 1fvjC 1dsdS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | THERE 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. |
-Components
#1: Protein | 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.86 % |
---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 289 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 10, 1995 / Details: YALE MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.7→1.78 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.36 / % possible all: 84.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 1DSD Resolution: 1.7→50 Å / Cross valid method: YES / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.78 Å
|