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Yorodumi- PDB-1ho4: CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE IN COMPLEX ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ho4 | ||||||
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Title | CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE IN COMPLEX WITH PYRIDOXINE 5'-PHOSPHATE AND INORGANIC PHOSPHATE | ||||||
Components | PYRIDOXINE 5'-PHOSPHATE SYNTHASE | ||||||
Keywords | BIOSYNTHETIC PROTEIN / TIM Barrel / Open-Closed Transition / Enzyme-Product Complex / Water Channel | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 1ho4.cif.gz | 206.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ho4.ent.gz | 165.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ho4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ho4_validation.pdf.gz | 481.7 KB | Display | wwPDB validaton report |
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Full document | 1ho4_full_validation.pdf.gz | 507.2 KB | Display | |
Data in XML | 1ho4_validation.xml.gz | 46.6 KB | Display | |
Data in CIF | 1ho4_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/1ho4 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/1ho4 | HTTPS FTP |
-Related structure data
Related structure data | 1ho1C 1hoiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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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: Chemical | #3: Chemical | ChemComp-PXP / #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: 3.05 Å3/Da / Density % sol: 59.68 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 54860 / Num. obs: 110743 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.6 / Num. unique all: 13071 / Rsym value: 0.208 / % possible all: 95.7 |
Reflection | *PLUS Num. obs: 54860 / Num. measured all: 110743 |
Reflection shell | *PLUS % possible obs: 95.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HOI Resolution: 2.3→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: 56.6 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d |