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Yorodumi- PDB-1m5w: 1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m5w | ||||||
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Title | 1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate | ||||||
Components | Pyridoxal phosphate biosynthetic protein pdxJ | ||||||
Keywords | BIOSYNTHETIC PROTEIN / TIM barrel / protein-substrate complex / multi-binding states | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Yeh, J.I. / Du, S. / Pohl, E. / Cane, D.E. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Multistate Binding in Pyridoxine 5'-Phosphate Synthase: 1.96 A Crystal Structure in Complex with 1-deoxy-D-xylulose phosphate Authors: Yeh, J.I. / Du, S. / Pohl, E. / Cane, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m5w.cif.gz | 380.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m5w.ent.gz | 312.9 KB | Display | PDB format |
PDBx/mmJSON format | 1m5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m5w_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 1m5w_full_validation.pdf.gz | 507.5 KB | Display | |
Data in XML | 1m5w_validation.xml.gz | 47.6 KB | Display | |
Data in CIF | 1m5w_validation.cif.gz | 71.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/1m5w ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m5w | HTTPS FTP |
-Related structure data
Related structure data | 1ho4S 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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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 26421.340 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PDXJ / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A794 #2: Chemical | ChemComp-DXP / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.35 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, PEG 1000, glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 297K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 21, 2000 |
Radiation | Monochromator: wiggler / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. all: 163858 / Num. obs: 157249 / % possible obs: 96 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.6 / Num. unique all: 13719 / Rsym value: 0.304 / % possible all: 84.4 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 96 % / Num. measured all: 494561 |
Reflection shell | *PLUS % possible obs: 84.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HO4 Resolution: 1.96→6 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.4 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→6 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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