[English] 日本語
Yorodumi
- PDB-4zt7: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zt7
TitleTrypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-[(4R)-6,8-dichloro-1,2,3,4-tetrahydroquinolin-4-yl]-N'-(5-fluoro-3H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1717)
ComponentsMethionyl-tRNA synthetase
KeywordsLigase/Ligase Inhibitor / ligase / aminoacyl-tRNA synthetase / aaRS / MetRS / Trypanosoma brucei / protein-inhibitor complex / Ligase-Ligase Inhibitor complex
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ciliary plasm / ATP binding / cytoplasm
Similarity search - Function
Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Methionine-tRNA synthetase, type 2 / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Methionyl/Leucyl tRNA synthetase ...Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Methionine-tRNA synthetase, type 2 / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4RC / METHIONINE / methionine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKoh, C.-Y. / Hol, W.G.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acs Infect Dis. / Year: 2016
Title: 5-Fluoroimidazo[4,5-b]pyridine Is a Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-tRNA Synthetase Inhibitors.
Authors: Zhang, Z. / Koh, C.Y. / Ranade, R.M. / Shibata, S. / Gillespie, J.R. / Hulverson, M.A. / Huang, W. / Nguyen, J. / Pendem, N. / Gelb, M.H. / Verlinde, C.L. / Hol, W.G. / Buckner, F.S. / Fan, E.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Jan 15, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 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: Methionyl-tRNA synthetase
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8339
Polymers122,8692
Non-polymers9637
Water9,134507
1
A: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8185
Polymers61,4351
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0144
Polymers61,4351
Non-polymers5803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.627, 105.842, 207.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Methionyl-tRNA synthetase


Mass: 61434.707 Da / Num. of mol.: 2 / Fragment: UNP residues 237-773 / Mutation: K456A, K457R, E458A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb10.70.6470 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38C91, methionine-tRNA ligase

-
Non-polymers , 5 types, 514 molecules

#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-4RC / N-[(4R)-6,8-dichloro-1,2,3,4-tetrahydroquinolin-4-yl]-N'-(5-fluoro-3H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine


Mass: 409.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19Cl2FN6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.0-2.3 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M sodium cacodylate
PH range: 6.0 to 6.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 20, 2013
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→37.8 Å / Num. obs: 75309 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.055 / Net I/σ(I): 15.3 / Num. measured all: 525460 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.454.30.8181.81881343630.5860.44699.3
12-37.860.02562409067710.01196.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.68 Å37.8 Å
Translation8.68 Å37.8 Å

-
Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
PHASER2.5.6phasing
REFMACrefmac_5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EG8

4eg8


Resolution: 2.4→37.8 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / Matrix type: sparse / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.207 / SU B: 13.988 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 3795 5 %RANDOM
Rwork0.2074 71386 --
obs0.2088 71386 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.87 Å2 / Biso mean: 37.923 Å2 / Biso min: 9.26 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å20 Å20 Å2
2---0.64 Å2-0 Å2
3----2.27 Å2
Refinement stepCycle: final / Resolution: 2.4→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8322 0 58 507 8887
Biso mean--41.05 32.64 -
Num. residues----1049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198614
X-RAY DIFFRACTIONr_bond_other_d0.0030.028104
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.95311714
X-RAY DIFFRACTIONr_angle_other_deg0.913318619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39751049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10423.436390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.434151380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.311556
X-RAY DIFFRACTIONr_chiral_restr0.0650.21295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219740
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021996
X-RAY DIFFRACTIONr_mcbond_it0.5611.754205
X-RAY DIFFRACTIONr_mcbond_other0.5611.754204
X-RAY DIFFRACTIONr_mcangle_it0.9752.6225251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.4-2.4620.3422700.3085181545699.9080.308
2.462-2.5290.3012610.28507953401000.28
2.529-2.6020.3182690.264489851671000.264
2.602-2.6820.2782450.25482650711000.25
2.682-2.7690.2752610.237462248831000.237
2.769-2.8660.282250.229453947641000.229
2.866-2.9740.242340.214433245661000.214
2.974-3.0940.2592310.218421444451000.218
3.094-3.2310.2522170.201402942461000.201
3.231-3.3870.2282100.198383540451000.198
3.387-3.5690.2091800.197370038801000.197
3.569-3.7830.2331860.198350736931000.198
3.783-4.0420.2031810.186326834491000.186
4.042-4.3610.1831800.1693061324299.9690.169
4.361-4.7710.2011610.16283729981000.16
4.771-5.3240.2021390.178259627351000.178
5.324-6.1270.2541050.215232524301000.215
6.127-7.4550.2141000.214198420841000.214
7.455-10.3440.187870.158158116681000.158
10.344-37.7970.233530.226972104098.5580.226
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)
11.6683-1.8948-1.0463.35621.0441.52640.10930.2382-0.1176-0.2505-0.1550.2109-0.0111-0.24020.04570.1098-0.01940.05580.0562-0.02370.0758-6.539-11.882-56.149
21.9386-0.8115-0.83363.75730.86742.3339-0.0745-0.0034-0.0355-0.02430.03960.02850.1151-0.10970.03490.0705-0.01180.05680.0092-0.01230.08681.5-14.826-50.758
36.9613-0.815-1.88954.28510.97885.83030.02910.4347-1.2902-0.50910.06290.61451.0344-0.058-0.09190.3758-0.0831-0.05120.2222-0.20160.584-26.946-9.055-42.772
42.6029-1.6009-1.12832.85780.29813.2612-0.0209-0.0205-0.110.23830.06490.407-0.1569-0.6725-0.0440.06490.02740.09750.1710.00080.1595-27.25812.935-30.784
50.82180.5232-0.456810.34590.08713.45160.14710.36690.2656-0.4265-0.0571.2102-0.018-0.6228-0.09010.25480.05410.07070.26580.04910.2473-27.47614.852-40.015
62.2587-0.6022-1.04030.71530.90312.6587-0.1073-0.2719-0.12630.21410.06930.08360.11020.07150.0380.10620.02330.05170.0380.00940.1349-30.32312.10810.832
75.96585.52450.04512.19490.97032.581-0.0584-0.0533-0.67380.007-0.03360.72610.5964-0.81670.0920.334-0.0239-0.03490.50810.0380.4413-59.520.78910.815
82.4097-0.8184-1.35692.2280.64972.4504-0.04590.0538-0.08110.076-0.02280.0289-0.0767-0.25030.06870.03610.01470.05910.0304-0.00320.1531-37.41322.7244.994
92.1385-0.5354-1.06861.79240.14442.8877-0.1686-0.0751-0.33170.20560.02060.14830.35960.10080.1480.14640.00530.06390.0094-0.01060.1511-15.292-3.983-10.434
1014.5371.25379.69274.22290.824212.67330.5648-0.3186-1.46510.3169-0.078-0.94260.24150.6529-0.48680.67710.0498-0.01860.3960.06820.6859-15.865-17.128-3.433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 380
2X-RAY DIFFRACTION2A381 - 546
3X-RAY DIFFRACTION3A547 - 608
4X-RAY DIFFRACTION4A609 - 731
5X-RAY DIFFRACTION5A732 - 767
6X-RAY DIFFRACTION6B-4 - 351
7X-RAY DIFFRACTION7B352 - 400
8X-RAY DIFFRACTION8B401 - 546
9X-RAY DIFFRACTION9B547 - 754
10X-RAY DIFFRACTION10B755 - 767

+
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