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- PDB-2x3f: Crystal Structure of the Methicillin-Resistant Staphylococcus aur... -
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Open data
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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. | ||||||
![]() | PANTHOTHENATE SYNTHETASE | ||||||
![]() | LIGASE / ATP-BINDING / NUCLEOTIDE-BINDING / PANTOTHENATE BIOSYNTHESIS | ||||||
Function / homology | ![]() pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.8 KB | Display | ![]() |
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PDB format | ![]() | 190.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Strain: MRSA252 / Plasmid: PDEST14 / Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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