+Open data
-Basic information
Entry | Database: PDB / ID: 1adj | ||||||
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Title | HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDINE | ||||||
Components | HISTIDYL-TRNA SYNTHETASE | ||||||
Keywords | COMPLEX (TRNA SYNTHETASE/PEPTIDE) / AMINO ACID / HISTIDINE / COMPLEX (TRNA SYNTHETASE-PEPTIDE) / COMPLEX (TRNA SYNTHETASE-PEPTIDE) complex | ||||||
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 / MIR / Resolution: 2.7 Å | ||||||
Authors | Cusack, S. / Aberg, A. | ||||||
Citation | 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 | 1adj.cif.gz | 329.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1adj.ent.gz | 272.2 KB | Display | PDB format |
PDBx/mmJSON format | 1adj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1adj_validation.pdf.gz | 413.9 KB | Display | wwPDB validaton report |
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Full document | 1adj_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 1adj_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 1adj_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/1adj ftp://data.pdbj.org/pub/pdb/validation_reports/ad/1adj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 47125.918 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: HISTIDINE PRESENT IN THE ACTIVE SITE / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P56194, histidine-tRNA ligase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HIS / #4: 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: 2.4 Å3/Da / Density % sol: 48.83 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 24, 1994 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 49630 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.7→20 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.2 / % possible all: 97 |
Reflection | *PLUS Num. measured all: 214739 |
Reflection shell | *PLUS % possible obs: 97 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.7→20 Å
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection Rfree: 2502 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |