[English] 日本語
Yorodumi
- PDB-1li5: Crystal Structure of Cysteinyl-tRNA Synthetase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1li5
TitleCrystal Structure of Cysteinyl-tRNA Synthetase
ComponentsCYSTEINYL-TRNA SYNTHETASE
KeywordsLIGASE / TRNA SYNTHETASE / CYSTEINE / E.COLI
Function / homology
Function and homology information


cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / aminoacyl-tRNA ligase activity / ligase activity / zinc ion binding / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases / Cysteinyl-tRNA synthetase, class Ia, DALR / DALR domain / DALR_2 / Cysteine-tRNA ligase / Cysteinyl-tRNA synthetase/mycothiol ligase / tRNA synthetases class I, catalytic domain / tRNA synthetases class I (C) catalytic domain / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / HUPs ...Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases / Cysteinyl-tRNA synthetase, class Ia, DALR / DALR domain / DALR_2 / Cysteine-tRNA ligase / Cysteinyl-tRNA synthetase/mycothiol ligase / tRNA synthetases class I, catalytic domain / tRNA synthetases class I (C) catalytic domain / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / HUPs / Four Helix Bundle (Hemerythrin (Met), subunit A) / Rossmann-like alpha/beta/alpha sandwich fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cysteine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsNewberry, K.J. / Hou, Y.-M. / Perona, J.J.
Citation
Journal: EMBO J. / Year: 2002
Title: Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase
Authors: Newberry, K.J. / Hou, Y.-M. / Perona, J.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary Diffraction Analysis of Escherichia Coli Cysteinyl-tRNA Synthetase
Authors: Newberry, K.J. / Kohn, J. / Hou, Y.-M. / Perona, J.J.
History
DepositionApr 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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: CYSTEINYL-TRNA SYNTHETASE
B: CYSTEINYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6734
Polymers104,5422
Non-polymers1312
Water1,838102
1
A: CYSTEINYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3362
Polymers52,2711
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYSTEINYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3362
Polymers52,2711
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.160, 119.160, 144.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212
DetailsThe active biological unit is a monomer

-
Components

#1: Protein CYSTEINYL-TRNA SYNTHETASE / E.C.6.1.1.16 / Cysteine--tRNA ligase / CysRS / transfer RNA-Cys synthetase


Mass: 52271.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P21888, cysteine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.45 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 8000, 200 MM magnesium acetate, 1MM DTT, cacodylate, 5MM ATP, 10MM cysteine. 100 MM BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
210 mMHEPES1droppH7.4
350 mM1dropNaCl
41 mMdithiothreitol1drop
55 mM1dropMgCl2
65 mMATP1drop
710 mMcysteine1drop
815-17 %PEG80001reservoir
9100 mMsodium cacodylate1reservoirpH6.5
10200 mMmagnesium acetate1reservoir
112 %t-butanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 13, 2001
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. all: 46671 / Num. obs: 45949 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.6 / Num. unique all: 6494 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 45 Å

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→19.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2449639.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 4632 10.1 %RANDOM
Rwork0.245 ---
all0.2451 46671 --
obs0.2451 45854 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.9212 Å2 / ksol: 0.325178 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---1 Å20 Å2
3---2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 2 102 5780
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it9.22
X-RAY DIFFRACTIONc_scangle_it10.922.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3265 449 9.4 %
Rwork0.2758 6932 -
obs-4140 99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Rfactor obs: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09
LS refinement shell
*PLUS
Rfactor obs: 0.2758

+
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://pdbjlvh1.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