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Open data
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Basic information
Entry | Database: PDB / ID: 1kmm | ||||||
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Title | HISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDYL-ADENYLATE | ||||||
![]() | HISTIDYL-TRNA SYNTHETASE | ||||||
![]() | AMINOACYL-TRNA SYNTHASE / LIGASE / SYNTHETASE | ||||||
Function / homology | ![]() histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / protein homodimerization activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Arnez, J.G. / Francklyn, C.S. / Moras, D. | ||||||
![]() | ![]() Title: The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase. Authors: Arnez, J.G. / Augustine, J.G. / Moras, D. / Francklyn, C.S. #1: ![]() Title: Crystal Structure of Histidyl-tRNA Synthetase from Escherichia Coli Complexed with Histidyl-Adenylate Authors: Arnez, J.G. / Harris, D.C. / Mitschler, A. / Rees, B. / Francklyn, C.S. / Moras, D. #2: ![]() Title: Crystallization of Histidyl-tRNA Synthetase from Escherichia Coli Authors: Francklyn, C. / Harris, D. / Moras, D. #3: ![]() Title: Primary Structure of Histidine-tRNA Synthetase and Characterization of Hiss Transcripts Authors: Freedman, R. / Gibson, B. / Donovan, D. / Biemann, K. / Eisenbeis, S. / Parker, J. / Schimmel, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 358.8 KB | Display | ![]() |
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PDB format | ![]() | 290.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 53.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 47085.316 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HAM / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 68 % Description: MERGED DATA SET DATA SCALING SOFTWARE : MARSCALE | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.6→12 Å / Num. obs: 66471 / % possible obs: 85.4 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 69.7 Å2 / Rmerge(I) obs: 0.0956 / Net I/σ(I): 24 | ||||||||||||||||||||||||
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4 / % possible all: 47.5 | ||||||||||||||||||||||||
Reflection | *PLUS Num. measured all: 183629 | ||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 47.5 % |
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Processing
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Refinement | Resolution: 2.6→12 Å / σ(F): 3
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Displacement parameters | Biso mean: 46.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.353 |