+Open data
-Basic information
Entry | Database: PDB / ID: 1a2m | ||||||
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Title | OXIDIZED DSBA AT 2.7 ANGSTROMS RESOLUTION, CRYSTAL FORM III | ||||||
Components | DISULFIDE BOND FORMATION PROTEIN | ||||||
Keywords | 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Martin, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a2m.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a2m.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 1a2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a2m_validation.pdf.gz | 433.4 KB | Display | wwPDB validaton report |
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Full document | 1a2m_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 1a2m_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1a2m_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/1a2m ftp://data.pdbj.org/pub/pdb/validation_reports/a2/1a2m | HTTPS FTP |
-Related structure data
Related structure data | 1a2jC 1a2lC 1fvkS 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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2 |
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Unit cell |
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-Components
#1: Protein | 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 / | |
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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: 2.61 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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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 RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 10, 1996 / 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: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FVK Resolution: 2.7→50 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 1
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Displacement parameters | Biso mean: 24.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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