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Yorodumi- PDB-2a0n: Crystal structure of Imidazole glycerol phosphate synthase subuni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a0n | ||||||
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Title | Crystal structure of Imidazole glycerol phosphate synthase subunit hisF (EC 4.1.3.-) (tm1036) from Thermotoga maritima at 1.64 A resolution | ||||||
Components | Imidazole glycerol phosphate synthase subunit hisF | ||||||
Keywords | LYASE / tm1036 / Imidazole glycerol phosphate synthase subunit hisF / EC 4.1.3.- / IGP / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / amino acid biosynthetic process / lyase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Imidazole glycerol phosphate synthase subunit hisF (EC 4.1.3.-) (tm1036) from Thermotoga maritima at 1.64 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a0n.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a0n.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 2a0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a0n_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 2a0n_full_validation.pdf.gz | 435.8 KB | Display | |
Data in XML | 2a0n_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 2a0n_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/2a0n ftp://data.pdbj.org/pub/pdb/validation_reports/a0/2a0n | HTTPS FTP |
-Related structure data
Related structure data | 1vh7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29215.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisF / Production host: Escherichia coli (E. coli) References: UniProt: Q9X0C6, Lyases; Carbon-carbon lyases; Oxo-acid-lyases | ||||||
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#2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.33 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.9 Details: 0.2None Nal, 20.0% PEG-3350, No Buffer, pH 6.9, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979748 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2004 Details: Flat Mirror; Side-deflecting monochromator (Si 111) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Flat Mirror; Side-deflecting monochromator (Si 111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979748 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.64→48.31 Å / Num. obs: 53271 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 6.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.014 / Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1vh7 Resolution: 1.64→48.31 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.353 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE ADDITIONAL DENSITY NEAR CYS-9 HAS BEEN MODELED AS AN UNL, UNKNOWN LIGAND. THIS RESIDUE IS COVALENTLY BOUND TO SG OF CYS-9.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.454 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→48.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.683 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 22.2282 Å / Origin y: 79.1115 Å / Origin z: 37.306 Å
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Refinement TLS group | Selection: all |