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- PDB-1adj: HISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDINE -

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Basic information

Entry
Database: PDB / ID: 1adj
TitleHISTIDYL-TRNA SYNTHETASE IN COMPLEX WITH HISTIDINE
ComponentsHISTIDYL-TRNA SYNTHETASEHistidine—tRNA ligase
KeywordsCOMPLEX (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
Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / Histidine--tRNA ligase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 Å
AuthorsCusack, S. / Aberg, A.
CitationJournal: 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
DepositionFeb 18, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTIDYL-TRNA SYNTHETASE
B: HISTIDYL-TRNA SYNTHETASE
C: HISTIDYL-TRNA SYNTHETASE
D: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,51312
Polymers188,5044
Non-polymers1,0098
Water4,288238
1
A: HISTIDYL-TRNA SYNTHETASE
B: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7566
Polymers94,2522
Non-polymers5044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-51 kcal/mol
Surface area34790 Å2
MethodPISA
2
C: HISTIDYL-TRNA SYNTHETASE
D: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7566
Polymers94,2522
Non-polymers5044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-52 kcal/mol
Surface area34810 Å2
MethodPISA
3
A: HISTIDYL-TRNA SYNTHETASE
B: HISTIDYL-TRNA SYNTHETASE
hetero molecules

C: HISTIDYL-TRNA SYNTHETASE
D: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,51312
Polymers188,5044
Non-polymers1,0098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_546-x+1/2,y-1/2,-z+11
Buried area19250 Å2
ΔGint-109 kcal/mol
Surface area66360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.300, 214.700, 49.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.95697, 0.285443, 0.052261), (0.290173, 0.939469, 0.182201), (0.002911, 0.189525, -0.981872)80.95425, -16.69062, 46.84542
2given(0.998128, -0.0596, -0.013706), (-0.061083, -0.982496, -0.175985), (-0.002977, 0.176493, -0.984297)2.32469, 126.15175, 48.35885
3given(-0.975678, 0.217446, -0.027742), (-0.21624, -0.975484, -0.040888), (-0.035953, -0.033895, 0.998778)86.06161, 128.7951, 3.43501

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Components

#1: Protein
HISTIDYL-TRNA SYNTHETASE / Histidine—tRNA ligase


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 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlhistidyl-tRNA1drop
24.3 mg/mltRNAHis1drop
33-10 mM1dropMgCl2
41 mM1dropNaN3
515 %(w/v)ammonium sulphate1drop
6100 mMbis-tris propane1drop
750 %satammonium sulphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 24, 1994 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→20 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.277 -5 %RANDOM
Rwork0.217 ---
obs0.217 46757 99 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13280 0 20 238 13538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.497
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 2502
Solvent computation
*PLUS
Displacement parameters
*PLUS

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