+Open data
-Basic information
Entry | Database: PDB / ID: 5hbq | ||||||
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Title | C63D mutant of the rhodanese domain of YgaP | ||||||
Components | Inner membrane protein YgaP | ||||||
Keywords | TRANSFERASE / S-nitrosylation / 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. / Nakamura, T. / Kwiatkowski, W. / Maslennikov, I. / Choe, S. / Lipton, S.A. / Riek, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein. Authors: Eichmann, C. / Tzitzilonis, C. / Nakamura, T. / Kwiatkowski, W. / Maslennikov, I. / Choe, S. / Lipton, S.A. / Riek, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hbq.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hbq.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 5hbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hbq_validation.pdf.gz | 424.7 KB | Display | wwPDB validaton report |
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Full document | 5hbq_full_validation.pdf.gz | 424.7 KB | Display | |
Data in XML | 5hbq_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 5hbq_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/5hbq ftp://data.pdbj.org/pub/pdb/validation_reports/hb/5hbq | HTTPS FTP |
-Related structure data
Related structure data | 5hblSC 5hboC 5hbpC 5lamC 5laoC 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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-Components
#1: Protein | Mass: 14058.774 Da / Num. of mol.: 1 / Fragment: Rhodanese domain, UNP residues 2-109 / Mutation: C63D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ygaP, b2668, JW2643 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Star / References: UniProt: P55734 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.97 % |
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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 4, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.66→38 Å / Num. obs: 13404 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.3 | |||||||||||||||
Reflection shell | Resolution: 1.66→1.75 Å / Redundancy: 4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / Num. unique all: 1947 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HBL Resolution: 1.66→38 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.046 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / 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: 19.07 Å2
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Refinement step | Cycle: 1 / Resolution: 1.66→38 Å
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Refine LS restraints |
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