[English] 日本語
Yorodumi
- PDB-1hc7: Prolyl-tRNA synthetase from Thermus thermophilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hc7
TitleProlyl-tRNA synthetase from Thermus thermophilus
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 / aminoacyl-tRNA synthetase multienzyme complex / 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--tRNA ligase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.43 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
DepositionApr 26, 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)218,5138
Polymers218,2524
Non-polymers2624
Water13,295738
1
A: PROLYL-TRNA SYNTHETASE
B: PROLYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2574
Polymers109,1262
Non-polymers1312
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)109,2574
Polymers109,1262
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)132.300, 191.100, 125.100
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(0.854501, 0.519239, 0.014762), (0.519444, -0.854269, -0.020053), (0.002199, 0.024803, -0.99969)-11.4256, 37.1653, 221.631
2given(0.221515, 0.808838, 0.544713), (0.829419, -0.450035, 0.330958), (0.512831, 0.378483, -0.770555)-40.6175, -0.0687, 93.68
3given(0.652301, 0.437916, 0.618654), (-0.56748, 0.823239, 0.015612), (-0.502463, -0.361258, 0.785508)-44.0437, 10.3581, 126.523
DetailsTHERE ARE TWO BIOMOLECULES (DIMERS) IN THE ASYMMTERICUNIT FORMED BY CHAINS A + B AND CHAINS C + D RESPECTIVELY.

-
Components

#1: Protein
PROLYL-TRNA SYNTHETASE / PROLYL-TRNA LIGASE


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-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 738 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.9 / Details: SEE REFERENCE 2, pH 7.90

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.826
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826 Å / Relative weight: 1
ReflectionResolution: 2.43→15 Å / Num. obs: 117904 / % possible obs: 98.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.9 / % possible all: 93.1

-
Processing

Software
NameClassification
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RSPSphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.43→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: TETRAHEDRAL ZINC CO-ORDINATION TO FOUR CYSTEINES WAS RESTRAINED. SIDE-CHAIN ATOMS WITH OCCUPANCY 0 HAVE VERY POOR OR MISSING ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.234 5908 4.9 %RANDOM
Rwork0.206 ---
obs0.206 117862 98.6 %-
Solvent computationSolvent model: BULK SOLVENT / Bsol: 38.2446 Å2 / ksol: 0.330525 e/Å3
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.66 Å20 Å20 Å2
2---4.26 Å20 Å2
3---7.93 Å2
Refinement stepCycle: LAST / Resolution: 2.43→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14988 0 4 738 15730
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.286
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_it1.3051.5
X-RAY DIFFRACTIONc_mcangle_it3.5073
X-RAY DIFFRACTIONc_scbond_it2.1552
X-RAY DIFFRACTIONc_scangle_it4.944
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more