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Yorodumi- PDB-1uu1: Complex of Histidinol-phosphate aminotransferase (HisC) from Ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uu1 | ||||||
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Title | Complex of Histidinol-phosphate aminotransferase (HisC) from Thermotoga maritima (Apo-form) | ||||||
Components | HISTIDINOL-PHOSPHATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / HISTIDINE BIOSYNTHESIS / AMINOTRANSFERASE / PYRIDOXAL PHOSPHATE | ||||||
Function / homology | Function and homology information histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / L-histidine biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Vega, M.C. / Fernandez, F.J. / Lehman, F. / Wilmanns, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural Studies of the Catalytic Reaction Pathway of a Hyperthermophilic Histidinol-Phosphate Aminotransferase Authors: Fernandez, F.J. / Vega, M.C. / Lehmann, F. / Sandmeier, E. / Gehring, H. / Christen, P. / Wilmanns, M. #1: Journal: J.Mol.Biol. / Year: 2001 Title: Crystal Structure of Histidinol Phosphate Aminotransferase (Hisc) from Escherichia Coli, and its Covalent Complex with Pyridoxal-5'-Phosphate and L-Histidinol Phosphate Authors: Sivaraman, J. / Li, Y. / Larocque, R. / Schrag, J.D. / Cygler, M. / Matte, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uu1.cif.gz | 287.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uu1.ent.gz | 234.1 KB | Display | PDB format |
PDBx/mmJSON format | 1uu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uu1_validation.pdf.gz | 490.5 KB | Display | wwPDB validaton report |
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Full document | 1uu1_full_validation.pdf.gz | 557.2 KB | Display | |
Data in XML | 1uu1_validation.xml.gz | 61.7 KB | Display | |
Data in CIF | 1uu1_validation.cif.gz | 83.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/1uu1 ftp://data.pdbj.org/pub/pdb/validation_reports/uu/1uu1 | HTTPS FTP |
-Related structure data
Related structure data | 1h1cSC 1uu0C 1uu2C 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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-Components
#1: Protein | Mass: 39350.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: PHOSPHATE ANION ATTACHED PER CHAIN / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9X0D0, histidinol-phosphate transaminase #2: Chemical | ChemComp-PMP / #3: Chemical | ChemComp-HSA / #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: 2.4 Å3/Da / Density % sol: 44.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting 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: X13 / Wavelength: 0.8042 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8042 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20 Å / Num. obs: 49556 / % possible obs: 90.6 % / Redundancy: 1.25 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.0885 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.35→2.45 Å / Redundancy: 1 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.22 / % possible all: 91.3 |
Reflection | *PLUS Highest resolution: 2.35 Å / Lowest resolution: 20 Å / Redundancy: 2.3 % / Num. measured all: 120299 / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 91.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H1C Resolution: 2.38→19.67 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / ksol: 0.36114 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.38→19.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.53 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 49260 / % reflection Rfree: 4.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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