[English] 日本語
Yorodumi
- PDB-4qrd: Structure of Methionyl-tRNA Synthetase in complex with N-(1H-benz... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qrd
TitleStructure of Methionyl-tRNA Synthetase in complex with N-(1H-benzimidazol-2-ylmethyl)-N'-(2,4-dichlorophenyl)-6-(morpholin-4-yl)-1,3,5-triazine-2,4-diamine
ComponentsMethionyl-tRNA synthetase
KeywordsLIGASE/LIGASE INHIBITOR / protein synthesis / aminoacyl-tRNA synthetase / aminoacylation / cytosol / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / HUPs / Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta ...Methionyl-trna Synthetase; domain 2 / Methionyl-trna Synthetase; domain 2 - #10 / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / HUPs / Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsLi, X. / Hilgers, M.T. / Stidham, M. / Brown-Driver, V. / Shaw, K.J. / Finn, J.
CitationJournal: to be published
Title: Discovery and SAR of a Novel Series of Pyrimidine Antibacterials Targeting Methionyl-tRNA Synthetase
Authors: Li, X. / Hilgers, M.T. / Stidham, M. / Brown-Driver, V. / Shaw, K.J. / Finn, J.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Methionyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6133
Polymers63,1171
Non-polymers4962
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.438, 76.726, 118.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Methionyl-tRNA synthetase


Mass: 63117.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: metG, CH52_03385 / Production host: Escherichia coli (E. coli) / References: UniProt: W8U1H8, methionine-tRNA ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-3BJ / N-(1H-benzimidazol-2-ylmethyl)-N'-(2,4-dichlorophenyl)-6-(morpholin-4-yl)-1,3,5-triazine-2,4-diamine


Mass: 471.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20Cl2N8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: PEG 3350, Tris pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→21.25 Å / Num. all: 28282 / % possible obs: 69.04 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.97-2.06169.8
2.07-2.18171.3
2.19-2.33171.8
2.34-2.52172.6
2.53-2.76173
2.77-3.1172.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.356 / Cor.coef. Fo:Fc: 0.666
Highest resolutionLowest resolution
Rotation3 Å21.46 Å
Translation3 Å21.46 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREP5phasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.14data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→21.25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.2596 / WRfactor Rwork: 0.1911 / FOM work R set: 0.7849 / SU B: 11.127 / SU ML: 0.161 / SU R Cruickshank DPI: 0.3337 / SU Rfree: 0.2612 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.326 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2829 1426 5 %RANDOM
Rwork0.2007 ---
all0.205 28282 --
obs0.205 28282 69.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.89 Å2 / Biso mean: 25.556 Å2 / Biso min: 7.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.97→21.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 33 263 4516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224373
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.9655939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8745520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36124.67212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.40415744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4931518
X-RAY DIFFRACTIONr_chiral_restr0.1280.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023357
X-RAY DIFFRACTIONr_nbd_refined0.2260.22152
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2243
X-RAY DIFFRACTIONr_metal_ion_refined0.0230.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3180.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6880.222
X-RAY DIFFRACTIONr_mcbond_it0.7731.52697
X-RAY DIFFRACTIONr_mcangle_it1.22424214
X-RAY DIFFRACTIONr_scbond_it1.82232005
X-RAY DIFFRACTIONr_scangle_it2.3814.51724
LS refinement shellResolution: 1.97→2.019 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 94 -
Rwork0.282 1758 -
all-1852 -
obs--62.21 %
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)
11.33340.6339-0.25480.5241-0.0720.2662-0.01070.0771-0.1053-0.0811-0.00620.0275-0.051-0.02480.01690.02980.0218-0.0165-0.2072-0.0120.047511.197-12.395-26.486
21.1133-1.0034-1.07372.38892.56194.203-0.0438-0.2508-0.25850.1324-0.06090.06720.3101-0.11220.1047-0.0006-0.017-0.0191-0.12020.04350.01094.613-13.212-5.346
31.6083-0.31620.77091.2922-1.69292.3009-0.10580.01190.04070.0306-0.04480.0505-0.16540.14770.15060.01940.0384-0.005-0.2140.00880.0311-9.7371.461-14.746
42.1321-4.084-0.809311.38262.10690.92830.3194-0.0271-0.0294-0.2391-0.39470.0537-0.0035-0.09460.07530.00370.0151-0.0257-0.1199-0.002-0.0411-14.51512.122-22.834
58.57071.3863-4.40842.0576-1.986.01630.3274-0.18450.280.2313-0.1246-0.1141-0.53450.2331-0.20280.1092-0.0753-0.0162-0.2539-0.0189-0.035815.3637.295-6.504
61.0151-0.2365-0.67860.11010.39361.4620.0777-0.15030.0665-0.0530.00890.0509-0.2573-0.1575-0.08670.05750.01-0.0093-0.22690.0068-0.0011.1960.026-12.051
71.00810.1766-0.12370.38030.14161.45120.0983-0.1499-0.05490.0131-0.01190.0172-0.1710.0879-0.08640.00660.0131-0.0126-0.180.01380.013113.223-5.281-13.989
858.3033-9.135419.41934.9497-5.6678.42540.1218-0.4314-0.5411-0.59860.00290.28450.5744-0.5348-0.12460.0155-0.0135-0.09220.0146-0.00250.01362.5422.549-40.018
90.80670.0879-0.43880.1661-0.31090.7985-0.01220.086-0.01190.01090.0188-0.00010.03410.0232-0.00660.05620.0053-0.0226-0.1878-0.0246-0.000935.16-0.891-44.574
103.31630.38250.74581.0898-1.49443.35460.00460.0105-0.3349-0.1234-0.0602-0.13860.3354-0.03760.05550.0550.06670.0266-0.2668-0.0445-0.001839.455-12.134-41.875
112.3736-1.00182.51361.2676-2.27294.4007-0.04990.0307-0.1212-0.14440.04260.0883-0.03320.06760.00720.03380.00830.0249-0.1423-0.0048-0.0365-9.6010.076-9.075
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 97
2X-RAY DIFFRACTION2A98 - 117
3X-RAY DIFFRACTION3A118 - 136
4X-RAY DIFFRACTION4A137 - 161
5X-RAY DIFFRACTION5A174 - 192
6X-RAY DIFFRACTION6A193 - 234
7X-RAY DIFFRACTION7A235 - 302
8X-RAY DIFFRACTION8A303 - 317
9X-RAY DIFFRACTION9A318 - 475
10X-RAY DIFFRACTION10A476 - 520
11X-RAY DIFFRACTION11A162 - 173

+
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