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Yorodumi- PDB-5hbl: Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitros... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hbl | ||||||
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Title | Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated | ||||||
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 / MIR / Resolution: 1.617 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 | 5hbl.cif.gz | 35.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hbl.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hbl_validation.pdf.gz | 294.6 KB | Display | wwPDB validaton report |
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Full document | 5hbl_full_validation.pdf.gz | 294.6 KB | Display | |
Data in XML | 5hbl_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 5hbl_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/5hbl ftp://data.pdbj.org/pub/pdb/validation_reports/hb/5hbl | HTTPS FTP |
-Related 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: 14075.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / 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: 2.08 Å3/Da / Density % sol: 40.81 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.617→52.31 Å / Num. obs: 14075 / % possible obs: 97.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.617→1.623 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.9 / % possible all: 70 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.617→38.07 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.674 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 18.652 Å2
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Refinement step | Cycle: 1 / Resolution: 1.617→38.07 Å
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Refine LS restraints |
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