+Open data
-Basic information
Entry | Database: PDB / ID: 1ho1 | ||||||
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Title | CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE | ||||||
Components | PYRIDOXINE 5'-PHOSPHATE SYNTHASE | ||||||
Keywords | BIOSYNTHETIC PROTEIN / TIM barrel | ||||||
Function / homology | Function and homology information pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å | ||||||
Authors | Garrido-Franco, M. / Laber, B. / Huber, R. / Clausen, T. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Structural basis for the function of pyridoxine 5'-phosphate synthase. Authors: Franco, M.G. / Laber, B. / Huber, R. / Clausen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ho1.cif.gz | 199.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ho1.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ho1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ho1_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 1ho1_full_validation.pdf.gz | 481.6 KB | Display | |
Data in XML | 1ho1_validation.xml.gz | 45.2 KB | Display | |
Data in CIF | 1ho1_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/1ho1 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/1ho1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is an octamer generated from the tetramer in the asymmetric unit by the operations: x,-y,-z |
-Components
#1: Protein | Mass: 26290.143 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PDXJ / Plasmid: PASK-IBA3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P0A794 #2: 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: 3.15 Å3/Da / Density % sol: 60.89 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG6000, 2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: microseeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 16, 1999 |
Radiation | Monochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 87995 / Num. obs: 345047 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.8 / Num. unique all: 48550 / Rsym value: 0.452 / % possible all: 98.5 |
Reflection | *PLUS Num. obs: 87995 / Num. measured all: 345047 |
Reflection shell | *PLUS % possible obs: 98.5 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2→20 Å / Isotropic thermal model: Anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
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Displacement parameters | Biso mean: 39.7 Å2 | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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