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Yorodumi- PDB-4c5l: Structure of the pyridoxal kinase from Staphylococcus aureus in c... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 4c5l | ||||||
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| Title | Structure of the pyridoxal kinase from Staphylococcus aureus in complex with pyridoxal | ||||||
Components | PHOSPHOMETHYLPYRIMIDINE KINASE | ||||||
Keywords | TRANSFERASE / RIBOKINASE | ||||||
| Function / homology | Function and homology informationphosphomethylpyrimidine kinase activity / hydroxymethylpyrimidine kinase activity / pyridoxal kinase / thiamine biosynthetic process / nucleotide binding / cytosol Similarity search - Function | ||||||
| Biological species | STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Nodwell, M. / Alte, F. / Sieber, S.A. / Schneider, S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014Title: 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. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4c5l.cif.gz | 413.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4c5l.ent.gz | 344.9 KB | Display | PDB format |
| PDBx/mmJSON format | 4c5l.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4c5l_validation.pdf.gz | 505.4 KB | Display | wwPDB validaton report |
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| Full document | 4c5l_full_validation.pdf.gz | 517.9 KB | Display | |
| Data in XML | 4c5l_validation.xml.gz | 42 KB | Display | |
| Data in CIF | 4c5l_validation.cif.gz | 58.6 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/4c5l ftp://data.pdbj.org/pub/pdb/validation_reports/c5/4c5l | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 4c5jSC ![]() 4c5kC ![]() 4c5mC ![]() 4c5nC 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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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS oper:
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Components
| #1: Protein | Mass: 29811.793 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)Production host: ![]() References: UniProt: Q99W31, UniProt: A0A0H3JTP0*PLUS, pyridoxal kinase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PXL / | #5: Water | ChemComp-HOH / | Has protein modification | Y | Sequence details | FIRST AMINO ACID 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: 2.28 Å3/Da / Density % sol: 45 % / Description: NONE |
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| Crystal grow | Details: 50MM HEPES PH 7.6, 2M NH4SO4 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / 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: 1.85→43.81 Å / Num. obs: 90725 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.65 |
| Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.1 / % possible all: 97 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 4C5J Resolution: 1.85→43.81 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.071 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 29.128 Å2
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| Refinement step | Cycle: LAST / Resolution: 1.85→43.81 Å
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| Refine LS restraints |
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STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
X-RAY DIFFRACTION
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