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- PDB-4e51: Crystal structure of a histidyl-tRNA synthetase HisRS from Burkho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4.0E+51 | ||||||
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Title | Crystal structure of a histidyl-tRNA synthetase HisRS from Burkholderia thailandensis bound to histidine | ||||||
![]() | Histidine--tRNA ligase | ||||||
![]() | LIGASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / aminoacylation / tRNA activation / charged tRNA / histidyl-adenylate / ATP-dependent / tRNA synthetase / aaRS | ||||||
Function / homology | ![]() histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms. Authors: Moen, S.O. / Edwards, T.E. / Dranow, D.M. / Clifton, M.C. / Sankaran, B. / Van Voorhis, W.C. / Sharma, A. / Manoil, C. / Staker, B.L. / Myler, P.J. / Lorimer, D.D. #1: ![]() Title: Combining functional and structural genomics to sample the essential Burkholderia structome. Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 313.4 KB | Display | ![]() |
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PDB format | ![]() | 252.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.8 KB | Display | ![]() |
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Full document | ![]() | 461.4 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 40.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sp1C ![]() 3tzeC ![]() 4ex5C ![]() 4g6zC ![]() 4griC ![]() 1httS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 9 - 501 / Label seq-ID: 30
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Components
#1: Protein | Mass: 51937.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: ButhA.00063.a.A1 PS01164 at 31 mg/mL with 5 mM L-histidine against Wizard III A3 focus screen, 350 mM magnesium formate, 12% PEG 3350 with 20% glycerol as cryo-protectant, crystal tracking ...Details: ButhA.00063.a.A1 PS01164 at 31 mg/mL with 5 mM L-histidine against Wizard III A3 focus screen, 350 mM magnesium formate, 12% PEG 3350 with 20% glycerol as cryo-protectant, crystal tracking ID 230808g3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976484 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→50 Å / Num. all: 34582 / Num. obs: 34582 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 56.022 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.34 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1HTT Resolution: 2.65→19.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2221 / WRfactor Rwork: 0.1875 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8262 / SU B: 21.915 / SU ML: 0.214 / SU R Cruickshank DPI: 0.4772 / SU Rfree: 0.2805 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.477 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.15 Å2 / Biso mean: 51.8046 Å2 / Biso min: 24.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→19.61 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 11800 / Refine-ID: X-RAY DIFFRACTION / Type: RESTRAINTS / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.65→2.719 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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