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Yorodumi- PDB-5hpa: The crystal of rhodanese domain of YgaP treated with sodium thios... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hpa | ||||||
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Title | The crystal of rhodanese domain of YgaP treated with sodium thiosulfate | ||||||
Components | Inner membrane protein YgaP | ||||||
Keywords | TRANSFERASE / S-sulfhydration. rhodanese | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Eichmann, C. / Tzitzilonis, C. / Kwiatkowski, W. / Riek, R. | ||||||
Citation | Journal: To Be Published Title: S-Sulfhydration of the Catalytic Cysteine in the Rhodanese Domain of YgaP is a Complex Dynamical Process. Authors: Eichmann, C. / Tzitzilonis, C. / Kwiatkowski, W. / Riek, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hpa.cif.gz | 39.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hpa.ent.gz | 25 KB | Display | PDB format |
PDBx/mmJSON format | 5hpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hpa_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 5hpa_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 5hpa_validation.xml.gz | 8 KB | Display | |
Data in CIF | 5hpa_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/5hpa ftp://data.pdbj.org/pub/pdb/validation_reports/hp/5hpa | HTTPS FTP |
-Related structure data
Related structure data | 5hboS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 14078.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ygaP, b2668, JW2643 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: P55734 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.91 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M sodium acetate in 0.1 M Tris HCl pH 8.5, and 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.127 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→37.84 Å / Num. obs: 13126 / % possible obs: 98.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.66→1.75 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.057 / Mean I/σ(I) obs: 16.2 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HBO Resolution: 1.66→37.84 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.564 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.094 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.007 Å2
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Refinement step | Cycle: 1 / Resolution: 1.66→37.84 Å
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Refine LS restraints |
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