+Open data
-Basic information
Entry | Database: PDB / ID: 1vh5 | ||||||
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Title | Crystal structure of a putative thioesterase | ||||||
Components | Hypothetical protein ydiI | ||||||
Keywords | Structural genomics / unknown function / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information 1,4-dihydroxy-2-naphthoyl-CoA hydrolase / acyl-CoA hydrolase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / phylloquinone biosynthetic process / menaquinone biosynthetic process / peroxisome / hydrolase activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.34 Å | ||||||
Authors | Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Structural analysis of a set of proteins resulting from a bacterial genomics project Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vh5.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vh5.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 1vh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vh5_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 1vh5_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 1vh5_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1vh5_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/1vh5 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/1vh5 | HTTPS FTP |
-Related structure data
Related structure data | 1o60C 1o61C 1o62C 1o63C 1o64C 1o65C 1o66C 1o67C 1o68C 1o69C 1o6bC 1o6cC 1o6dC 1vgtC 1vguC 1vgvC 1vgwC 1vgxC 1vgyC 1vgzC 1vh0C 1vh1C 1vh2C 1vh3C 1vh4C 1vh6C 1vh7C 1vh8C 1vh9C 1vhaC 1vhcC 1vhdC 1vheC 1vhfC 1vhgC 1vhjC 1vhkC 1vhlC 1vhmC 1vhoC 1vhqC 1vhsC 1vhtC 1vhuC 1vhvC 1vhwC 1vhxC 1vhyC 1vhzC 1vi0C 1vi1C 1vi2C 1vi3C 1vi4C 1vi5C 1vi6C 1vi8C 1vi9C 1viaC 1vicC 1vimC 1viqC 1visC 1viuC 1vivC 1vixC 1viyC 1vizC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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: 16325.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YDII, B1686 / Production host: Escherichia coli (E. coli) / References: UniProt: P77781 #2: 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: 2.12 Å3/Da / Density % sol: 41.9 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9794, 1.5418 | |||||||||
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Detector | Type: RIGAKU / Detector: IMAGE PLATE | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.28→52.71 Å / Num. obs: 67624 / % possible obs: 94.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.6 | |||||||||
Reflection shell | Resolution: 1.28→1.35 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 94.6 | |||||||||
Reflection | *PLUS Highest resolution: 1.47 Å / Num. obs: 47125 / % possible obs: 98.6 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.068 | |||||||||
Reflection shell | *PLUS % possible obs: 91.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.34→12.27 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Solvent computation | Solvent model: Babinet bulk solvent correction / Bsol: 59.753 Å2 / ksol: 0.631 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.94 Å2
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Refine Biso | Class: all / Treatment: anisotropic | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→12.27 Å
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Refine LS restraints |
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Software | *PLUS Version: 4 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.47 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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