+Open data
-Basic information
Entry | Database: PDB / ID: 1h4v | ||||||
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Title | HISTIDYL-TRNA SYNTHETASE from Thermus Thermophilus (ligand free) | ||||||
Components | HISTIDYL-TRNA SYNTHETASEHistidine—tRNA ligase | ||||||
Keywords | TRNA SYNTHETASE / CLASS IIA AMINOACYL-TRNA SYNTHETASE / ATP + L-HISTIDINE TRNA(HIS)-> AMP + PPI + L-HISTIDYL-TRNA(HIS) | ||||||
Function / homology | Function and homology information histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Cusack, S. / Yaremchuk, A. / Tukalo, M. | ||||||
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: Biochemistry / Year: 1997 Title: Crystal Structure Analysis of the Activation of Histidine by Thermus Thermophilus Histidyl-tRNA Synthetase Authors: Aberg, A. / Yaremchuk, A. / Tukalo, M. / Rasmussen, B. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h4v.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h4v.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 1h4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/1h4v ftp://data.pdbj.org/pub/pdb/validation_reports/h4/1h4v | HTTPS FTP |
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-Related structure data
Related structure data | 1h4qC 1h4sC 1h4tC 1hc7C 1adjS 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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Unit cell |
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-Components
#1: Protein | Mass: 47125.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: LIGAND FREE FORM OF THE ENZYME / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 References: UniProt: P56194, UniProt: P62374*PLUS, histidine-tRNA ligase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE OF T. THERMOPHILUS HISTIDYL-TRNA SYNTHETASE IS GIVEN IN BIOCHEMISTRY 36, 3084 - 3094, ...THE SEQUENCE OF T. THERMOPHIL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: DESCRIBED IN REFERENCE 1., pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / pH: 7.6 / 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: ESRF / Beamline: ID2 / Wavelength: 0.99 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→12 Å / Num. obs: 39592 / % possible obs: 86.7 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.9 / % possible all: 72.1 |
Reflection | *PLUS Num. obs: 17744 / Num. measured all: 39592 |
Reflection shell | *PLUS % possible obs: 72.1 % / Rmerge(I) obs: 0.137 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ADJ Resolution: 2.4→12 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 57-62 AND 117-120 ARE DISORDERED. OTHER RESIDUES WITH SIDE-CHAIN ATOMS WITH ZERO OCCUPANCY ARE POORLY ORDERED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.1 Å2 / ksol: 0.44 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→12 Å
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Refine LS restraints |
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Xplor file |
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