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- PDB-1kmn: HISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDINOL AND ATP -

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Basic information

Entry
Database: PDB / ID: 1kmn
TitleHISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDINOL AND ATP
ComponentsHISTIDYL-TRNA SYNTHETASEHistidine—tRNA ligase
KeywordsAMINOACYL-TRNA SYNTHASE / LIGASE / SYNTHETASE
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
Histidyl-anticodon-binding / 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 / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily ...Histidyl-anticodon-binding / 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 / tRNA synthetase class II core domain (G, H, P, S and T) / 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
ADENOSINE-5'-TRIPHOSPHATE / L-histidinol / Histidine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsArnez, J.G. / Francklyn, C.S. / Moras, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
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: Journal: Embo J. / Year: 1995
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: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of Histidyl-tRNA Synthetase from Escherichia Coli
Authors: Francklyn, C. / Harris, D. / Moras, D.
#3: Journal: J.Biol.Chem. / Year: 1985
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
DepositionMay 9, 1997Processing site: BNL
Revision 1.0Dec 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2015Group: Non-polymer description
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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)190,93912
Polymers188,3414
Non-polymers2,5978
Water43224
1
A: HISTIDYL-TRNA SYNTHETASE
B: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4696
Polymers94,1712
Non-polymers1,2994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-18 kcal/mol
Surface area28520 Å2
MethodPISA
2
C: HISTIDYL-TRNA SYNTHETASE
D: HISTIDYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4696
Polymers94,1712
Non-polymers1,2994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-27 kcal/mol
Surface area29090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.900, 107.300, 107.200
Angle α, β, γ (deg.)114.10, 97.40, 90.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.211038, -0.015998, -0.977347), (-0.020306, -0.999579, 0.020746), (-0.977267, 0.024224, 0.210624)2.35111, 9.22819, 1.53649
2given(-0.999999, -0.000972, 0.00062), (-0.000972, 0.999999, -0.000447), (-0.00062, -0.000447, -1)-0.0791, -9.81098, -0.14376
3given(0.205806, 0.01538, 0.978472), (-0.01291, -0.999747, 0.01843), (0.978508, -0.016425, -0.205555)-2.47854, -0.32692, -1.80982

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Components

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


Mass: 47085.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Description: INDUCTION WITH IPTG / Plasmid: PHRS-7 / Gene (production host): HISS / Production host: Escherichia coli (E. coli) / Variant (production host): TRP-LAC / References: UniProt: P60906, histidine-tRNA ligase
#2: Chemical
ChemComp-HSO / L-histidinol


Type: L-peptide linking / Mass: 142.179 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12N3O
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.3 Å3/Da / Density % sol: 68 %
Crystal growpH: 7.4
Details: SLIGHT CONTRACTION DUE TO CRYO (-143 DEG C), pH 7.4
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.07-0.1 Menzyme1drop
350 mMhistidinol1drop
43 mMATP1drop
50.1 Mcitrate1reservoir
60.2 Mammonium acetate1reservoir
730 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.94
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 3, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.6→16 Å / Num. obs: 63562 / % possible obs: 84.4 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 71 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 18.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 5 / % possible all: 82.5
Reflection
*PLUS
Num. measured all: 116502
Reflection shell
*PLUS
% possible obs: 82.5 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MARXDSdata reduction
MARSCALEdata scaling
X-PLORphasing
RefinementResolution: 2.8→13 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.348 -2.5 %
Rwork0.249 --
obs0.249 38015 64 %
Displacement parametersBiso mean: 44.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11543 0 164 24 11731
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.894
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.04
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.606
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
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.506 68 2.6 %
Rwork0.406 2546 -
obs--35 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.04
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.606
LS refinement shell
*PLUS
Rfactor obs: 0.406

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