[English] 日本語
Yorodumi- PDB-1uu2: Histidinol-phosphate aminotransferase (HisC) from Thermotoga mari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uu2 | ||||||
---|---|---|---|---|---|---|---|
Title | Histidinol-phosphate aminotransferase (HisC) from Thermotoga maritima (apo-form) | ||||||
Components | HISTIDINOL-PHOSPHATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / HISTIDINE BIOSYNTHESIS / AMINOTRANSFERASE / PYRIDOXAL PHOSPHATE / COMPLETE PROTEOME AMINOTRANSFERASE | ||||||
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: 2.8 Å | ||||||
Authors | Vega, M.C. / Fernandez, F.J. / Lehmann, 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1uu2.cif.gz | 144.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1uu2.ent.gz | 113.3 KB | Display | PDB format |
PDBx/mmJSON format | 1uu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uu2_validation.pdf.gz | 461.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1uu2_full_validation.pdf.gz | 499.2 KB | Display | |
Data in XML | 1uu2_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 1uu2_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/1uu2 ftp://data.pdbj.org/pub/pdb/validation_reports/uu/1uu2 | HTTPS FTP |
-Related structure data
Related structure data | 1h1cSC 1uu0C 1uu1C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39350.945 Da / Num. of mol.: 2 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 | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.8→20 Å / Num. obs: 15921 / % possible obs: 91.7 % / Redundancy: 2.5 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.8 / % possible all: 99.3 |
Reflection | *PLUS Highest resolution: 2.85 Å / Lowest resolution: 20 Å / Redundancy: 2.5 % / Num. measured all: 57136 / Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS % possible obs: 99.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H1C Resolution: 2.8→19.91 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / ksol: 0.244716 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. reflection obs: 14772 / % reflection Rfree: 8.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|