[English] 日本語
Yorodumi
- PDB-6o3f: Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o3f
TitleCrystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis with complexed with L-lysine and a difluoro cyclohexyl chromone ligand
ComponentsLysine--tRNA ligase
KeywordsLIGASE / SSGCID / KRS / nucleotide binding / Aminoacyl TRNA Ligase Activity / Lysine TRNA Ligase Activity / ATP Binding / Lysyl TRNA Aminoacylation / strain UCH-1/proctitis / strain D/UW-3/Cx / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / nucleic acid binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II ...Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / 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) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-FYB / LYSINE / DI(HYDROXYETHYL)ETHER / Lysine--tRNA ligase
Similarity search - Component
Biological speciesChlamydia trachomatis serovar L2b
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis with complexed with L-lysine and a difluoro cyclohexyl chromone ligand
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionFeb 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,16546
Polymers121,2192
Non-polymers3,94644
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18030 Å2
ΔGint-49 kcal/mol
Surface area39500 Å2
Unit cell
Length a, b, c (Å)95.490, 57.280, 138.190
Angle α, β, γ (deg.)90.000, 95.190, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase / LysRS


Mass: 60609.441 Da / Num. of mol.: 2 / Fragment: ChtrA.00612.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis serovar L2b (strain UCH-1/proctitis) (bacteria)
Strain: UCH-1/proctitis / Gene: lysS, CTLon_0150 / Plasmid: ChtrA.00612.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0BAN6, lysine-tRNA ligase

-
Non-polymers , 7 types, 413 molecules

#2: Chemical ChemComp-FYB / ~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide


Mass: 355.308 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16F3NO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.47
Details: ChtrA.00612.a.B1.PW38393 at 25.76 mg/ml was incubated with 3 mM l-lysine, 3 mM DDD01510706, then was mixed 1:1 MorpheusB6opt1(d4): 9.63% (w/v) PEG 8000, 19.27% (v/v) ethylene glycol, 0.03 M ...Details: ChtrA.00612.a.B1.PW38393 at 25.76 mg/ml was incubated with 3 mM l-lysine, 3 mM DDD01510706, then was mixed 1:1 MorpheusB6opt1(d4): 9.63% (w/v) PEG 8000, 19.27% (v/v) ethylene glycol, 0.03 M each sodium fluoride, sodium bromide, sodium iodide, 0.1 M MOPS/HEPES-Na, pH=7.47. Tray: 305770d4, puck: wyo4-6.

-
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: Feb 7, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→45.55 Å / Num. obs: 58695 / % possible obs: 99.8 % / Redundancy: 3.782 % / Biso Wilson estimate: 43.037 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.099 / Χ2: 0.999 / Net I/σ(I): 12.46 / Num. measured all: 222013 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.463.8060.622.1716344429742940.7920.72299.9
2.46-2.533.8130.4982.7216098422242220.8390.581100
2.53-2.63.8080.4163.215509408040730.8890.48499.8
2.6-2.683.8080.3773.5315002394439400.9010.4499.9
2.68-2.773.8110.3174.2114769387638750.9280.369100
2.77-2.873.810.265.1414266375137440.9530.30299.8
2.87-2.983.8090.1966.713643358335820.9730.229100
2.98-3.13.80.1667.7813115345834510.9790.19399.8
3.1-3.243.8030.12910.0612607331633150.9870.15100
3.24-3.393.790.09812.8212205322632200.9920.11599.8
3.39-3.583.7820.07516.1611481304030360.9940.08799.9
3.58-3.793.7840.05919.6110802286128550.9960.06999.8
3.79-4.063.780.04922.6910226270827050.9970.05799.9
4.06-4.383.7740.0426.869545253825290.9980.04799.6
4.38-4.83.7620.03629.048761233523290.9980.04299.7
4.8-5.373.7440.03727.47867210721010.9980.04499.7
5.37-6.23.7320.04225.456987187118720.9980.05100
6.2-7.593.6870.03527.825848159015860.9980.04199.7
7.59-10.733.6270.02535.234599127112680.9990.02999.8
10.73-45.553.3510.02137.823397216980.9990.02596.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A74

3a74


Resolution: 2.4→45.55 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.75
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 1969 3.36 %RANDOM, 0
Rwork0.1628 ---
obs0.1643 58681 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.88 Å2 / Biso mean: 43.5579 Å2 / Biso min: 7.79 Å2
Refinement stepCycle: final / Resolution: 2.4→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8164 0 232 373 8769
Biso mean--62.66 44.19 -
Num. residues----1036
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46010.28841430.226739774120100
2.4601-2.52660.24111250.211940664191100
2.5266-2.60090.28831370.200240154152100
2.6009-2.68480.2581350.199739894124100
2.6848-2.78080.29151240.200440544178100
2.7808-2.89210.27551440.191240464190100
2.8921-3.02370.24781500.1940164166100
3.0237-3.18310.2841370.184940774214100
3.1831-3.38250.18141600.167839994159100
3.3825-3.64350.23271600.162640184178100
3.6435-4.010.1891390.144440614200100
4.01-4.58980.13871560.125840564212100
4.5898-5.78080.16841220.13841344256100
5.7808-45.55860.16191370.15044204434199
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)
10.30310.10180.05260.99780.39810.81080.03040.0174-0.0586-0.05660.0079-0.2180.19580.099-0.05480.30780.0364-0.00920.29750.04360.369729.2623-9.977938.2819
20.76960.15910.98420.62960.6191.86010.0917-0.0535-0.0759-0.0454-0.046-0.06450.3215-0.0546-0.06850.38660.00090.00630.24950.03640.279220.4802-17.948430.677
32.69730.20360.21682.548-0.90932.7614-0.06730.25660.2383-0.4061-0.0476-0.00820.047-0.00390.09260.47250.0558-0.03720.30710.00010.233711.4813-4.32242.0214
40.7238-0.1466-0.12420.7483-0.02040.9110.0338-0.0189-0.0106-0.032-0.06050.12310.0202-0.16370.02450.2301-0.0069-0.02180.2432-0.00180.23923.09234.444448.3956
54.04551.61180.26674.69230.00832.63270.03980.0060.14230.2157-0.0892-0.21880.00350.08570.06320.23040.0305-0.06330.2665-0.01780.226328.409217.995368.408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 116 through 436 )B116 - 436
2X-RAY DIFFRACTION2chain 'B' and (resid 437 through 601 )B437 - 601
3X-RAY DIFFRACTION3chain 'A' and (resid 4 through 167 )A4 - 167
4X-RAY DIFFRACTION4chain 'A' and (resid 168 through 601 )A168 - 601
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 115 )B5 - 115

+
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