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- PDB-1h4t: Prolyl-tRNA synthetase from Thermus thermophilus complexed with L... -

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Basic information

Entry
Database: PDB / ID: 1h4t
TitleProlyl-tRNA synthetase from Thermus thermophilus complexed with L-proline
ComponentsPROLYL-TRNA SYNTHETASE
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
PROLINE / Proline--tRNA ligase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 14, 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_site
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.pdbx_dist_value / _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_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_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: PROLYL-TRNA SYNTHETASE
B: PROLYL-TRNA SYNTHETASE
C: PROLYL-TRNA SYNTHETASE
D: PROLYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,97412
Polymers218,2524
Non-polymers7228
Water7,927440
1
A: PROLYL-TRNA SYNTHETASE
B: PROLYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4876
Polymers109,1262
Non-polymers3614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: PROLYL-TRNA SYNTHETASE
D: PROLYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4876
Polymers109,1262
Non-polymers3614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)132.570, 193.470, 125.240
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(0.855039, 0.518535, -0.005508), (0.518378, -0.854968, -0.01773), (-0.013903, 0.012305, -0.999828)-9.4397, 37.7063, 223.064
2given(0.221626, 0.817157, 0.532106), (0.828572, -0.445522, 0.339084), (0.514149, 0.365739, -0.775813)-40.4875, -0.3455, 93.9726
3given(0.619941, 0.454545, 0.639579), (-0.585689, 0.810493, -0.008306), (-0.52215, -0.369446, 0.76868)-44.3087, 13.8886, 129.9109

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Components

#1: Protein
PROLYL-TRNA SYNTHETASE


Mass: 54562.965 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURIFICATION DESCRIBED IN REFERENCE 2 / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB-8 / References: UniProt: Q5SM28*PLUS, proline-tRNA ligase
#2: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 3.68 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.9 / Details: SEE REFERENCE 2, pH 7.90

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. obs: 71108 / % possible obs: 99 % / Redundancy: 4 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 284962

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HC7 (LIGAND FREE PROLYL-TRNA SYNTHETASE)

1hc7


Resolution: 2.9→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: ZINC CO-ORDINATION TO FOUR CYSTEINES WAS RESTRAINED. SIDE-CHAINS ATOMS WITH OCCUPANCY ZERO HAVE POOR OR ABSENT ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3538 5 %RANDOM
Rwork0.2 ---
obs0.2 71108 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.4 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2---4.82 Å20 Å2
3---6.63 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14988 0 36 440 15464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0065
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_deg1.31
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_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.43
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it4.994
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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