[English] 日本語
Yorodumi
- PDB-4ycv: Crystal structure of cladosporin in complex with plasmodium lysyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ycv
TitleCrystal structure of cladosporin in complex with plasmodium lysyl-tRNA synthetase
ComponentsLysine--tRNA ligase
Keywordsligase/ligase inhibitor / Inhibitor / Complex / LysRS / cladosporin / ligase-ligase inhibitor complex
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, 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 ...Bacterial/eukaryotic lysine-tRNA ligase, 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
cladosporin / Lysine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.406 Å
AuthorsFang, P. / Wang, J. / Guo, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100136 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106134 United States
CitationJournal: Chem.Biol. / Year: 2015
Title: Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.
Authors: Fang, P. / Han, H. / Wang, J. / Chen, K. / Chen, X. / Guo, M.
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Other
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,2948
Polymers239,1254
Non-polymers1,1694
Water1267
1
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1474
Polymers119,5622
Non-polymers5852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-50 kcal/mol
Surface area39750 Å2
MethodPISA
2
C: Lysine--tRNA ligase
D: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1474
Polymers119,5622
Non-polymers5852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-48 kcal/mol
Surface area39370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.632, 112.098, 170.795
Angle α, β, γ (deg.)90.000, 99.300, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 59781.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate NF54) (eukaryote)
Strain: isolate NF54 / Gene: PFNF54_04763 / Production host: Escherichia coli (E. coli) / References: UniProt: W7JP72, lysine-tRNA ligase
#2: Chemical
ChemComp-KRS / cladosporin / (3R)-3-[[(2R,6S)-6-methyloxan-2-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one


Mass: 292.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: tri-sodium citrate, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.28357 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28357 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 34869 / % possible obs: 96.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 62.81 Å2 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.114 / Rrim(I) all: 0.229 / Χ2: 0.97 / Net I/av σ(I): 6.98 / Net I/σ(I): 4.5 / Num. measured all: 134325
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.523.70.53833880.7630.3120.6240.99294.5
3.52-3.663.70.44533370.8350.2590.5161.03893.4
3.66-3.833.70.35533650.9030.2030.410.99294.1
3.83-4.033.80.29533730.9260.1690.3411.04794
4.03-4.283.80.20734540.9610.1190.2390.94995.3
4.28-4.613.80.15534770.9760.0890.1791.00596.5
4.61-5.083.90.14835660.9810.0840.1710.97798.7
5.08-5.8140.19636060.9660.1110.2260.97799.6
5.81-7.3240.1836010.970.1020.2080.89499.5
7.32-504.10.05437020.9970.030.0620.8799.7

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PG3

4pg3


Resolution: 3.406→49.9 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 1708 4.94 %
Rwork0.2302 32841 -
obs0.2315 34549 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.92 Å2 / Biso mean: 58.4645 Å2 / Biso min: 25.85 Å2
Refinement stepCycle: final / Resolution: 3.406→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15170 0 84 7 15261
Biso mean--46.14 32.69 -
Num. residues----1935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715646
X-RAY DIFFRACTIONf_angle_d1.24621260
X-RAY DIFFRACTIONf_chiral_restr0.0472357
X-RAY DIFFRACTIONf_plane_restr0.0072765
X-RAY DIFFRACTIONf_dihedral_angle_d15.3395634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4058-3.52750.31771490.28853008315788
3.5275-3.66870.31461460.29373120326691
3.6687-3.83560.29251840.25593145332993
3.8356-4.03770.2991680.25823218338694
4.0377-4.29060.27431560.22693299345595
4.2906-4.62170.2331830.23298348197
4.6217-5.08630.22191800.20423385356599
5.0863-5.82140.24341840.242334313615100
5.8214-7.33060.25041860.242334153601100
7.3306-49.90560.22991720.190335223694100
Refinement TLS params.Method: refined / Origin x: 19.1776 Å / Origin y: -25.7328 Å / Origin z: 39.1554 Å
111213212223313233
T0.2548 Å2-0.039 Å20.0314 Å2-0.3347 Å20.0371 Å2--0.3284 Å2
L0.1665 °2-0.123 °2-0.0671 °2-0.3407 °20.2898 °2--0.4324 °2
S-0.0286 Å °0.0737 Å °-0.0075 Å °0.0195 Å °0.041 Å °-0.0124 Å °0.0542 Å °0.0418 Å °-0.0193 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA78 - 581
2X-RAY DIFFRACTION1allB77 - 581
3X-RAY DIFFRACTION1allC78 - 581
4X-RAY DIFFRACTION1allD79 - 581
5X-RAY DIFFRACTION1allE1 - 4
6X-RAY DIFFRACTION1allF1 - 7

+
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