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Yorodumi- PDB-1h4s: Prolyl-tRNA synthetase from Thermus thermophilus complexed with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h4s | |||||||||
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Title | Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG) and a prolyl-adenylate analogue | |||||||||
Components |
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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 / aminoacyl-tRNA synthetase multienzyme complex / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 | 1h4s.cif.gz | 245.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h4s.ent.gz | 190.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h4s_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1h4s_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1h4s_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 1h4s_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/1h4s ftp://data.pdbj.org/pub/pdb/validation_reports/h4/1h4s | HTTPS FTP |
-Related structure data
Related structure data | 1h4qC 1h4tC 1h4vC 1hc7SC C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.336459, 0.000265, -0.941698), Vector: Details | HOMODIMERIC PROLYL-TRNA SYNTHETASE AND THE RNA CHAIN | |
-Components
-Protein / RNA chain , 2 types, 3 molecules ABT
#1: Protein | Mass: 54562.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PURIFICATION OF PROTEIN DESCRIBED IN REFERENCE 2 / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB-8 / References: UniProt: Q5SM28*PLUS, proline-tRNA ligase #2: RNA chain | | Mass: 24927.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFICATION OF TRNAPRO DESCRIBED IN REFERENCE 3 / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB-8 |
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-Non-polymers , 4 types, 40 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: 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: 4.38 Å3/Da / Density % sol: 72 % |
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Crystal grow | pH: 7.9 / Details: SEE REFERENCE 3, pH 7.90 |
-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, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→20 Å / Num. obs: 221758 / % possible obs: 98.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 2.85→2.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.2 / % possible all: 96.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 55013 / Num. measured all: 221758 |
Reflection shell | *PLUS % possible obs: 96.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HC7 (LIGAND FREE PROLYL-TRNA SYNTHETASE) Resolution: 2.85→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→20 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |