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Yorodumi- PDB-4c5n: Structure of the pyridoxal kinase from Staphylococcus aureus in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c5n | ||||||
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Title | Structure of the pyridoxal kinase from Staphylococcus aureus in complex with AMP-PCP and pyridoxal | ||||||
Components | PHOSPHOMETHYLPYRIMIDINE KINASE | ||||||
Keywords | TRANSFERASE / RIBOKINASE | ||||||
Function / homology | Ribokinase / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-PXL / 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol / : Function and homology information | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Nodwell, M. / Alte, F. / Sieber, S.A. / Schneider, S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage. Authors: Nodwell, M.B. / Koch, M.F. / Alte, F. / Schneider, S. / Sieber, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c5n.cif.gz | 416.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c5n.ent.gz | 343.7 KB | Display | PDB format |
PDBx/mmJSON format | 4c5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c5n_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 4c5n_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4c5n_validation.xml.gz | 44.9 KB | Display | |
Data in CIF | 4c5n_validation.cif.gz | 61.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/4c5n ftp://data.pdbj.org/pub/pdb/validation_reports/c5/4c5n | HTTPS FTP |
-Related structure data
Related structure data | 4c5jSC 4c5kC 4c5lC 4c5mC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29811.793 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MU50 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: C8MK44, pyridoxal kinase |
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-Non-polymers , 5 types, 328 molecules
#2: Chemical | #3: Chemical | ChemComp-ACP / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-UEG / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | FIRST AMINOACID IS A GLY INSTEAD OF MET DUE TO REMOVAL OF THE AFFINITY TAG |
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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: 2.21 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Details: 50MM HEPES PH7.6, 2M NH4SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.26 Å / Num. obs: 107272 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 8.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C5J Resolution: 1.75→48.26 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.545 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 26.636 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→48.26 Å
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Refine LS restraints |
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