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- PDB-1h4q: Prolyl-tRNA synthetase from Thermus thermophilus complexed with t... -

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Basic information

Entry
Database: PDB / ID: 1h4q
TitleProlyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG), ATP and prolinol
Components
  • PROLYL-TRNA SYNTHETASE
  • TRNAPRO(CGG)
KeywordsAMINOACYL-TRNA SYNTHETASE / ATP + L-PROLINE + TRNA(PRO) AMP + PPI + L-PROLYL-TRNA(PRO) / CLASS II AMINOACYL-TRNA SYNTHETASE
Function / homology
Function and homology information


proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / Anticodon-binding domain ...C-terminal domain of ProRS / Proline-tRNA ligase, class IIa / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Translation Initiation Factor IF3 / Anticodon-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / 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 / PYRROLIDINE-2-CARBALDEHYDE / RNA / RNA (> 10) / Proline--tRNA ligase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYaremchuk, A. / Tukalo, M. / Cusack, S.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: A Succession of Substrate Induced Conformational Changes Ensures the Amino Acid Specificity of Thermus Thermophilus Prolyl-tRNA Synthetase: Comparison with Histidyl-tRNA Synthetase
Authors: Yaremchuk, A. / Tukalo, M. / Grotli, M. / Cusack, S.
#1: Journal: Embo J. / Year: 2000
Title: Crystal Structure of a Eukaryote/Archaeon-Like Prolyl-tRNA Synthetase and its Complex with tRNA (Pro)(Cgg)
Authors: Yaremchuk, A. / Cusack, S. / Tukalo, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallisation and Preliminary X-Ray Diffraction Analysis of Thermus Thermophilus Prolyl-tRNA Synthetase
Authors: Yaremchuk, A. / Cusack, S. / Tukalo, M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Improved Crystals of Thermus Thermophilus Prolyl-tRNA Synthetase Complexed with Cognate tRNA Obtained by Crystallisation from Precipitate
Authors: Yaremchuk, A. / Krikliviy, I. / Cusack, S. / Tukalo, M.
#4: Journal: Structure / Year: 1997
Title: TRNA(Pro) Recognition by Thermus Thermophilus Prolyl-tRNA Synthetase
Authors: Cusack, S. / Yaremchuk, A. / Krikliviy, I. / Tukalo, M.
History
DepositionMay 13, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLYL-TRNA SYNTHETASE
B: PROLYL-TRNA SYNTHETASE
T: TRNAPRO(CGG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,58911
Polymers134,0543
Non-polymers1,5368
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)141.290, 141.290, 237.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.322256, -0.002968, -0.946648), (-0.007627, -0.999954, 0.005731), (-0.946622, 0.009067, 0.322219)
Vector: 101.4571, 217.9021, 71.44)
DetailsHOMODIMERIC PROLYL-TRNA SYNTHETASE AND THE RNA CHAIN

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Components

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Protein / RNA chain , 2 types, 3 molecules ABT

#1: Protein PROLYL-TRNA SYNTHETASE


Mass: 54562.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PURIFICATION OF PROTEIN DESCRIBED IN REFERENCE 2 / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB-8 / References: UniProt: Q5SM28*PLUS, proline-tRNA ligase
#2: RNA chain TRNAPRO(CGG)


Mass: 24927.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFICATION OF TRNAPRO DESCRIBED IN REFERENCE 3 / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB-8

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Non-polymers , 5 types, 32 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PRI / PYRROLIDINE-2-CARBALDEHYDE / PROLINOL


Mass: 99.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / 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: 4.42 Å3/Da / Density % sol: 72 %
Crystal growpH: 7.9 / Details: SEE REFERENCE 3, pH 7.90

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 48648 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 3→3.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.7 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 184299
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS0.4refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HC7 (LIGAND FREE PROLYL-TRNA SYNTHETASE)

1hc7


Resolution: 3→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: TETRAHEDRAL CO-ORDINATION OF ZINC ATOMS TO FOUR CYSTEINES WAS RESTRAINED. SIDECHAIN ATOMS WITH OCCUPANCY ZERO HAVE POOR OR NISSING ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2452 5 %RANDOM
Rwork0.221 ---
obs0.221 48593 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.421 Å20 Å20 Å2
2--0.421 Å20 Å2
3----0.843 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7479 1436 88 24 9027
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.392
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.131.5
X-RAY DIFFRACTIONc_mcangle_it3.782
X-RAY DIFFRACTIONc_scbond_it3.52
X-RAY DIFFRACTIONc_scangle_it5.823
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4DNA_RNA_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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