+Open data
-Basic information
Entry | Database: PDB / ID: 2h1d | ||||||
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Title | ResA pH 9.25 | ||||||
Components | Thiol-disulfide oxidoreductase resA | ||||||
Keywords | OXIDOREDUCTASE / ResA / High pH / 9.25 / pH 9.25 / ResA hiph | ||||||
Function / homology | Function and homology information cytochrome complex assembly / disulfide oxidoreductase activity / antioxidant activity / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lewin, A. / Crow, A. / Oubrie, A. / Le Brun, N.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Molecular Basis for Specificity of the Extracytoplasmic Thioredoxin ResA. Authors: Lewin, A. / Crow, A. / Oubrie, A. / Le Brun, N.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h1d.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h1d.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 2h1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h1d_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 2h1d_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 2h1d_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 2h1d_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/2h1d ftp://data.pdbj.org/pub/pdb/validation_reports/h1/2h1d | HTTPS FTP |
-Related structure data
Related structure data | 2h19C 2h1aC 2h1bC 2h1gC 1su9S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 3
NCS ensembles :
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Details | The Biological Unit consists of a single ResA chain. |
-Components
#1: Protein | Mass: 15942.131 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: resA / Production host: Escherichia coli (E. coli) / References: UniProt: P35160 #2: Chemical | ChemComp-EDO / | #3: 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: 2.44 Å3/Da / Density % sol: 49.58 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.25 Details: Crystallized at pH 6.5 (30% PEG 4,000, 0.1 M MES, 0.2 M Ammonium Acetate) but then crystal soaked in a cryoprotectant at pH9.25 (MES component replaced by CHES pH 9.25) prior to data ...Details: Crystallized at pH 6.5 (30% PEG 4,000, 0.1 M MES, 0.2 M Ammonium Acetate) but then crystal soaked in a cryoprotectant at pH9.25 (MES component replaced by CHES pH 9.25) prior to data collection. The structure therefore represents a 'high pH soak'. See publication for further details., VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0688 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 7, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0688 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. all: 9636 / Num. obs: 9636 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.6 / Num. measured all: 4975 / Num. unique all: 1409 / Rsym value: 0.247 / % possible all: 98.6 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SU9 Resolution: 2.6→37.16 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.842 / SU B: 10.843 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.412 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.412 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→37.16 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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