+Open data
-Basic information
Entry | Database: PDB / ID: 1hc7 | ||||||
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Title | Prolyl-tRNA synthetase from Thermus thermophilus | ||||||
Components | PROLYL-TRNA SYNTHETASE | ||||||
Keywords | AMINOACYL-TRNA SYNTHETASE / ATP + L-PROLINE + TRNA(PRO) AMP + PPI + L-PROLYL-TRNA(PRO) / CLASS II AMINOACYL-TRNA SYNTHETASE | ||||||
Function / homology | Function and homology information proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.43 Å | ||||||
Authors | Yaremchuk, A. / Tukalo, M. / Cusack, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: A Succession of Substrate Induced Conformational Changes Ensures the Amino Acid Specificity of Thermus Thermophilus Prolyl-tRNA Synthetase: Comparison with Histidyl-tRNA Synthetase Authors: Yaremchuk, A. / Tukalo, M. / Grotli, M. / Cusack, S. #1: Journal: Embo J. / Year: 2000 Title: Crystal Structure of a Eukaryote/Archaeon-Like Prolyl-tRNA Synthetase and its Complex with tRNA (Pro)(Cgg) Authors: Yaremchuk, A. / Cusack, S. / Tukalo, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallisation and Preliminary X-Ray Diffraction Analysis of Thermus Thermophilus Prolyl-tRNA Synthetase Authors: Yaremchuk, A. / Cusack, S. / Tukalo, M. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Improved Crystals of Thermus Thermophilus Prolyl-tRNA Synthetase Complexed with Cognate tRNA Obtained by Crystallisation from Precipitate Authors: Yaremchuk, A. / Krikliviy, I. / Cusack, S. / Tukalo, M. #4: Journal: Structure / Year: 1997 Title: TRNA(Pro) Recognition by Thermus Thermophilus Prolyl-tRNA Synthetase Authors: Cusack, S. / Yaremchuk, A. / Krikliviy, I. / Tukalo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hc7.cif.gz | 381.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hc7.ent.gz | 322.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/1hc7 ftp://data.pdbj.org/pub/pdb/validation_reports/hc/1hc7 | HTTPS FTP |
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-Related 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THERE ARE TWO BIOMOLECULES (DIMERS) IN THE ASYMMTERICUNIT FORMED BY CHAINS A + B AND CHAINS C + D RESPECTIVELY. |
-Components
#1: Protein | Mass: 54562.965 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURIFICATION DESCRIBED IN REFERENCE 2 / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB-8 / References: UniProt: Q5SM28*PLUS, proline-tRNA ligase #2: Chemical | ChemComp-ZN / #3: 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: 3.72 Å3/Da / Density % sol: 65 % |
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Crystal grow | pH: 7.9 / Details: SEE REFERENCE 2, pH 7.90 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.826 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.826 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→15 Å / Num. obs: 117904 / % possible obs: 98.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 |
Reflection shell | Resolution: 2.43→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.9 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.43→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF Details: TETRAHEDRAL ZINC CO-ORDINATION TO FOUR CYSTEINES WAS RESTRAINED. SIDE-CHAIN ATOMS WITH OCCUPANCY 0 HAVE VERY POOR OR MISSING ELECTRON DENSITY
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Solvent computation | Solvent model: BULK SOLVENT / Bsol: 38.2446 Å2 / ksol: 0.330525 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.43→20 Å
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Refine LS restraints |
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Xplor file |
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