+Open data
-Basic information
Entry | Database: PDB / ID: 4y2m | ||||||
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Title | apo-GolB protein | ||||||
Components | Putative metal-binding transport protein | ||||||
Keywords | METAL TRANSPORT / Oxidized form / gold binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | ||||||
Authors | Wei, W. / Zhao, J. / Wang, F. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: Structural Insights and the Surprisingly Low Mechanical Stability of the Au-S Bond in the Gold-Specific Protein GolB Authors: Wei, W. / Sun, Y. / Zhu, M. / Liu, X. / Sun, P. / Wang, F. / Gui, Q. / Meng, W. / Cao, Y. / Zhao, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y2m.cif.gz | 22.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y2m.ent.gz | 16.6 KB | Display | PDB format |
PDBx/mmJSON format | 4y2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/4y2m ftp://data.pdbj.org/pub/pdb/validation_reports/y2/4y2m | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6927.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: DT2 / Gene: STMDT2_03511 / Production host: Escherichia coli (E. coli) / References: UniProt: U4MDP1, UniProt: A0A140UHB4*PLUS |
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#2: Chemical | ChemComp-AU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.0 M Ammonium citrate tribasic, 0.1 M BIS-TRIS propane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 22949 / % possible obs: 99.1 % / Redundancy: 9.64 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.25 |
-Processing
Software |
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Refinement | Resolution: 1.4→31.48 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.683 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.013 / 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: 23.106 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→31.48 Å
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Refine LS restraints |
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