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Yorodumi- PDB-1o66: Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o66 | ||||||
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Title | Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase | ||||||
Components | 3-methyl-2-oxobutanoate hydroxymethyltransferase | ||||||
Keywords | TRANSFERASE / structural genomics | ||||||
Function / homology | Function and homology information 3-methyl-2-oxobutanoate hydroxymethyltransferase / 3-methyl-2-oxobutanoate hydroxymethyltransferase activity / pantothenate biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Neisseria meningitidis serogroup B (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Se-Met SAD phasing / Resolution: 1.75 Å | ||||||
Authors | Structural GenomiX | ||||||
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 | 1o66.cif.gz | 245 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o66.ent.gz | 199.6 KB | Display | PDB format |
PDBx/mmJSON format | 1o66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o66_validation.pdf.gz | 485.8 KB | Display | wwPDB validaton report |
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Full document | 1o66_full_validation.pdf.gz | 502.5 KB | Display | |
Data in XML | 1o66_validation.xml.gz | 48.7 KB | Display | |
Data in CIF | 1o66_validation.cif.gz | 69.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/1o66 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/1o66 | HTTPS FTP |
-Related structure data
Related structure data | 1o60C 1o61C 1o62C 1o63C 1o64C 1o65C 1o67C 1o68C 1o69C 1o6bC 1o6cC 1o6dC 1vgtC 1vguC 1vgvC 1vgwC 1vgxC 1vgyC 1vgzC 1vh0C 1vh1C 1vh2C 1vh3C 1vh4C 1vh5C 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 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29878.980 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria) Species: Neisseria meningitidis / Strain: serogroup B / Gene: PANB, NMB0870 / Production host: Escherichia coli (E. coli) References: UniProt: Q9JZW6, 3-methyl-2-oxobutanoate hydroxymethyltransferase #2: Chemical | ChemComp-GOL / #3: 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: 2.57 Å3/Da / Density % sol: 52.16 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: hanging drop vapor diffusion / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS 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: 0.9795 Å |
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Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→43.44 Å / Num. all: 176101 / Num. obs: 176101 / % possible obs: 96 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.64→1.73 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.1 / % possible all: 96 |
Reflection shell | *PLUS % possible obs: 96 % / Redundancy: 4.4 % |
-Processing
Software |
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Refinement | Method to determine structure: Se-Met SAD phasing / Resolution: 1.75→43.44 Å / σ(F): 0
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Solvent computation | Solvent model: Babinet bulk solvent correction / Bsol: 295.383 Å2 / ksol: 0.999 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.772 Å2
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Refine Biso | Class: all / Treatment: isotropic | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→43.44 Å
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Refine LS restraints |
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Software | *PLUS Version: 4 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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