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Yorodumi- PDB-2x3f: Crystal Structure of the Methicillin-Resistant Staphylococcus aur... -
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-Basic information
Entry | Database: PDB / ID: 2x3f | ||||||
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Title | Crystal Structure of the Methicillin-Resistant Staphylococcus aureus Sar2676, a Pantothenate Synthetase. | ||||||
Components | PANTHOTHENATE SYNTHETASE | ||||||
Keywords | LIGASE / ATP-BINDING / NUCLEOTIDE-BINDING / PANTOTHENATE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2010 Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Purification, Crystallization and Data Collection of Methicillin-Resistant Staphylococcus Aureus Sar2676, a Pantothenate Synthetase. Authors: Seetharamappa, J. / Oke, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Carter, L. / Dorward, M. / Zawadzki, M. / Overton, I.M. / Van Niekirk, C.A.J. / Graham, S. / Botting, C.H. / Taylor, G. ...Authors: Seetharamappa, J. / Oke, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Carter, L. / Dorward, M. / Zawadzki, M. / Overton, I.M. / Van Niekirk, C.A.J. / Graham, S. / Botting, C.H. / Taylor, G.L. / White, M.F. / Barton, G.J. / Coote, P.J. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x3f.cif.gz | 234.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x3f.ent.gz | 190.9 KB | Display | PDB format |
PDBx/mmJSON format | 2x3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x3f_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2x3f_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2x3f_validation.xml.gz | 24 KB | Display | |
Data in CIF | 2x3f_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3f ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3f | HTTPS FTP |
-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C 1v8fS 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: 31584.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria) Strain: MRSA252 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6GDK5, pantoate-beta-alanine ligase (AMP-forming) #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: 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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 10% PEG 8000, 0.1M NA MES PH6.5, 0.2M ZN ACETATE WITH 11.5MGML-1 AMP-CPP. THE CRYSTALS WERE CRYOPROTECTED WITH OIL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 11, 2007 / Details: TOROIDAL ZERODUR MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→28.59 Å / Num. obs: 39073 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2 / % possible all: 98 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V8F Resolution: 1.95→28.59 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.227 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS THE STRUCTURE IS ONLY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS THE STRUCTURE IS ONLY ORDERED FROM RESIDUE 2 TO 282
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.115 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→28.59 Å
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Refine LS restraints |
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