+Open data
-Basic information
Entry | Database: PDB / ID: 1acv | ||||||
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Title | DSBA MUTANT H32S | ||||||
Components | DSBA | ||||||
Keywords | DISULFIDE OXIDOREDUCTASE / THIOREDOXIN FOLD / 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 / DIFFERENCE FOURIER / Resolution: 1.9 Å | ||||||
Authors | Guddat, L.W. / Martin, J.L. | ||||||
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: 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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1acv.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1acv.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 1acv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1acv_validation.pdf.gz | 409.6 KB | Display | wwPDB validaton report |
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Full document | 1acv_full_validation.pdf.gz | 410.2 KB | Display | |
Data in XML | 1acv_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1acv_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/1acv ftp://data.pdbj.org/pub/pdb/validation_reports/ac/1acv | HTTPS FTP |
-Related structure data
Related structure data | 1ac1C 1fvjC 1fvkSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9617, -0.2664, -0.0645), Vector: |
-Components
#1: Protein | Mass: 21103.955 Da / Num. of mol.: 2 / Mutation: H32S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: 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: 2.8 Å3/Da / Density % sol: 53.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.3 / Details: CACODYLATE PH 6.3, PEG 8K 25% | ||||||||||||||||||||||||||||||||||||||||||||||||
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: Sep 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 33192 / % possible obs: 94.1 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.06 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.6 / % possible all: 84.1 |
Reflection | *PLUS Num. measured all: 97285 |
Reflection shell | *PLUS % possible obs: 84.1 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 1.7 A STRUCTURE OF WILDTYPE OXIDISED DSBA (PDB ENTRY 1FVK) Resolution: 1.9→50 Å / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 Details: BULK SOLVENT CORRECTION USED SOLDEN=0.34 SOLRAD =0.25 A
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Displacement parameters | Biso mean: 33.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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