[English] 日本語
Yorodumi
- PDB-6ujd: Crystal structure of Cysteine-tRNA ligase from Elizabethkingia sp. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ujd
TitleCrystal structure of Cysteine-tRNA ligase from Elizabethkingia sp.
ComponentsCysteine--tRNA ligase
KeywordsLIGASE / SSGCID / Structural Genomics / Elizabethkingia sp / Cysteine-tRNA ligase / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
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 / Rossmann-like alpha/beta/alpha sandwich fold ...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 / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / PHOSPHATE ION / Cysteine--tRNA ligase
Similarity search - Component
Biological speciesElizabethkingia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Cysteine-tRNA ligase from Elizabethkingia sp.
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4278
Polymers56,9201
Non-polymers5077
Water1,44180
1
A: Cysteine--tRNA ligase
hetero molecules

A: Cysteine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,85516
Polymers113,8412
Non-polymers1,01414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5030 Å2
ΔGint-156 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.260, 78.260, 208.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-665-

HOH

21A-678-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Cysteine--tRNA ligase / Cysteinyl-tRNA synthetase / CysRS


Mass: 56920.367 Da / Num. of mol.: 1 / Fragment: ElmeA.00133.a.B1 / Mutation: T410A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia sp. (bacteria) / Gene: cysS, BMF97_00660 / Plasmid: ElmeA.00133.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0A1T3F4R2, cysteine-tRNA ligase

-
Non-polymers , 6 types, 87 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#5: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Anatrace MCSG-1 screen, condition A3: 10% (w/V) PEG 8000, 200mM sodium chloride, 100mM sodium phosphate dibasic / potassium phosphate monobasic pH 6.2: ElmeA.00133.a.B1.PS385583 at 8.47 ...Details: Anatrace MCSG-1 screen, condition A3: 10% (w/V) PEG 8000, 200mM sodium chloride, 100mM sodium phosphate dibasic / potassium phosphate monobasic pH 6.2: ElmeA.00133.a.B1.PS385583 at 8.47 mg/ml: cryo: 25% EG in 2 steps: tray 310561 a3: puck kzn9-2.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 8, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 20872 / % possible obs: 99.9 % / Redundancy: 7.936 % / Biso Wilson estimate: 68.633 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.045 / Χ2: 1.047 / Net I/σ(I): 29.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.678.170.5463.6914900.9180.583100
2.67-2.748.1860.4324.8114640.9560.462100
2.74-2.828.170.3286.2414350.9730.351100
2.82-2.918.120.2278.7214030.9890.243100
2.91-38.1520.18910.5413520.9920.202100
3-3.118.1470.14214.0712890.9930.152100
3.11-3.228.110.09919.0812590.9970.106100
3.22-3.368.0720.0823.3212360.9980.086100
3.36-3.518.0160.06129.1511570.9990.065100
3.51-3.687.9910.04636.7511360.9990.049100
3.68-3.887.9640.03744.1210800.9990.04100
3.88-4.117.9330.0314910200.9990.033100
4.11-4.397.8730.02955.1297210.031100
4.39-4.757.8310.02858.99070.9990.03100
4.75-5.27.7630.02659.6783510.028100
5.2-5.817.6620.02757.6676910.029100
5.81-6.717.4960.02958.566960.9990.031100
6.71-8.227.2670.02364.7159210.025100
8.22-11.636.8110.0267.6248810.022100
11.63-505.6060.02361.842920.9990.02593.6

-
Processing

Software
NameVersionClassification
PHENIX1.17rc2refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1li5-A as per Morda

1li5


Resolution: 2.6→38.46 Å / SU ML: 0.312 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2052
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 2166 10.42 %0
Rwork0.1755 ---
obs0.1798 20791 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 70.27 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 25 80 3316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043310
X-RAY DIFFRACTIONf_angle_d0.62294480
X-RAY DIFFRACTIONf_chiral_restr0.0437487
X-RAY DIFFRACTIONf_plane_restr0.0043570
X-RAY DIFFRACTIONf_dihedral_angle_d15.84561938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.31551440.24791183X-RAY DIFFRACTION99.92
2.66-2.730.28061410.21541223X-RAY DIFFRACTION99.93
2.73-2.80.24991370.21381215X-RAY DIFFRACTION99.93
2.8-2.880.25621280.1941232X-RAY DIFFRACTION99.93
2.88-2.980.27031640.21991189X-RAY DIFFRACTION99.93
2.98-3.080.32531430.21971224X-RAY DIFFRACTION99.93
3.08-3.210.2551440.20851210X-RAY DIFFRACTION99.93
3.21-3.350.26681260.21246X-RAY DIFFRACTION100
3.35-3.530.25361530.21230X-RAY DIFFRACTION100
3.53-3.750.24121370.18951243X-RAY DIFFRACTION100
3.75-4.040.22261480.1611240X-RAY DIFFRACTION100
4.04-4.440.18121600.13541231X-RAY DIFFRACTION100
4.44-5.080.16221550.13191260X-RAY DIFFRACTION100
5.09-6.40.20361450.16641297X-RAY DIFFRACTION100
6.41-38.460.1911410.18231402X-RAY DIFFRACTION99.42
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.507256317530.0945664764776-0.6428957253872.123536399750.02003242871973.638913065470.159079709634-0.00355597623501-0.0363593439616-0.0109322269414-0.1403440236920.260206657890.222496242185-0.282985621047-0.0280055937390.408809666658-0.0971690306824-0.06108117981070.462639261369-0.00692101741930.487264226926-14.86670689077.6449745097739.1146701552
23.18317359359-1.229207748410.4313333207282.01213014785-0.4907988649211.636243969270.207641417227-0.0229361380989-0.1582268203880.02204828190040.1135214796420.416601075430.0730598283147-0.469530861564-0.3559906443530.570144887547-0.132208766983-0.002319016462080.5470149316120.05030196831610.562165226844-33.060653344516.456484258740.0726970995
31.32295883199-0.854250127948-0.1471086330411.996636902480.04243419774220.8043591641010.09043110785210.0785387564567-0.1120966052420.0330350681285-0.00340127047164-0.055984745480.1281102760470.0797734970659-0.08392198993660.471854261172-0.0629550936138-0.0996391480910.551265757043-0.0469101177430.436239260163-8.14603404531-0.76531686041132.8385333449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 209 )
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 430 )

+
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