[English] 日本語
Yorodumi
- PDB-7ulz: Crystal Structure of Methionine-tRNA ligase / Methionyl-tRNA synt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ulz
TitleCrystal Structure of Methionine-tRNA ligase / Methionyl-tRNA synthetase (MetRS) from Pseudomonas aeruginosa PAO1
ComponentsMethionine--tRNA ligase
KeywordsLIGASE / SSGCID / Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS / Pseudomonas aeruginosa / tRNA(fMet) aminoacylation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. ...Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
METHIONINE / Methionine--tRNA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of Methionine-tRNA ligase / Methionyl-tRNA synthetase (MetRS) from Pseudomonas aeruginosa PAO1
Authors: Abendroth, J. / DeBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionApr 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5719
Polymers62,7491
Non-polymers8228
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.900, 167.900, 72.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 62749.160 Da / Num. of mol.: 1 / Fragment: PsaeA.10201.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: metG, PA3482 / Plasmid: PsaeA.10201.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HYC7, methionine-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.75 Å3/Da / Density % sol: 74.12 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Anatrace MCSG1 screen, condition D8: 1.5M Ammonium sulfate + BisTris/HCl pH 6.5: PsaeA.10201.a.B1.PW38931 at 23mg/ml + 3mM L-Methionine + 3mM AMP. Tray 320141 d7: cryo: 20% EG + compounds: puck egi5-5

-
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: Mar 10, 2022 / 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: 2.8→50 Å / Num. obs: 29094 / % possible obs: 99.9 % / Redundancy: 6.261 % / Biso Wilson estimate: 44.871 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.129 / Χ2: 0.889 / Net I/σ(I): 13.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.876.3230.622.8821230.9330.677100
2.87-2.956.3020.5433.3620890.9290.59399.9
2.95-3.046.3410.4334.1420190.9540.47299.9
3.04-3.136.3420.3524.9719510.9660.384100
3.13-3.236.30.3125.5119020.9770.3499.9
3.23-3.356.3120.2267.1318450.990.24799.9
3.35-3.476.3240.189.1317860.990.196100
3.47-3.616.330.13811.1117160.9950.15199.9
3.61-3.786.2830.1213.0916430.9940.13199.9
3.78-3.966.2830.10315.4415810.9940.113100
3.96-4.176.2890.08717.615000.9970.09599.9
4.17-4.436.2640.07220.3914240.9970.079100
4.43-4.736.2790.06722.3713280.9970.07399.9
4.73-5.116.2510.0623.5512650.9980.066100
5.11-5.66.2050.07121.3311600.9960.07899.9
5.6-6.266.1560.07221.1510420.9960.07899.9
6.26-7.236.1760.06323.529380.9970.069100
7.23-8.856.0310.04430.568020.9980.048100
8.85-12.525.8260.03438.696220.9990.038100
12.52-505.2680.03636.253580.9980.0496.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1 4487refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3h99 as per Morda

3h99


Resolution: 2.8→48.47 Å / SU ML: 0.3494 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1880 6.48 %0
Rwork0.175 27136 --
obs0.1766 29016 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.79 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4073 0 44 125 4242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434262
X-RAY DIFFRACTIONf_angle_d0.65265797
X-RAY DIFFRACTIONf_chiral_restr0.0425614
X-RAY DIFFRACTIONf_plane_restr0.006752
X-RAY DIFFRACTIONf_dihedral_angle_d13.64961519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.361530.28992057X-RAY DIFFRACTION99.33
2.88-2.960.27581230.26472080X-RAY DIFFRACTION99.82
2.96-3.060.27641460.25882050X-RAY DIFFRACTION99.64
3.06-3.160.2771480.23712069X-RAY DIFFRACTION99.69
3.17-3.290.29831360.22372082X-RAY DIFFRACTION99.37
3.29-3.440.22261440.21362073X-RAY DIFFRACTION99.77
3.44-3.620.2351660.20652047X-RAY DIFFRACTION99.64
3.62-3.850.18831390.1672072X-RAY DIFFRACTION99.95
3.85-4.150.16721410.14992097X-RAY DIFFRACTION99.91
4.15-4.560.14811530.12842097X-RAY DIFFRACTION99.96
4.56-5.220.1541370.12662115X-RAY DIFFRACTION100
5.22-6.580.18551510.16012110X-RAY DIFFRACTION99.91
6.58-48.470.14631430.13862187X-RAY DIFFRACTION99.4
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)
13.55345147017-0.699041276362.214938995144.326504241150.7938971432793.610974948330.230267656333-0.806264029224-0.5789330497140.340288359005-0.0492049722875-0.173841506452-0.3866505026340.522503326515-0.1985070655250.645301772822-0.0958582220426-0.03220095367760.804104532283-0.113400903320.359347869608-77.71320.4598.158
21.02219004109-0.47780016411-0.2800465444793.268336668080.1757713799431.70158517813-0.02371990575570.08511932406520.0854652939219-0.169511305172-0.0190142901716-0.344117201234-0.1563094505440.291679432170.05363554896860.356203769648-0.00910067012662-0.01038023476860.40618924548-0.04214681525920.228538668289-79.63416.2750.802
34.376629023361.582242100325.09239906640.6242385703341.760973378075.916119448410.01278718318320.34029038081-0.0435506898425-0.0438429947920.1482620780750.0734981478363-0.5069877805380.834346415341-0.1150805201260.821536982823-0.09487167323460.0839142654740.4864124323520.01797408415010.404690977511-72.37941.25716.003
40.4986452199480.692525380251-0.5033122320941.059330453040.2987034811640.873893417460.010263590145-0.09723259074430.07927259756590.0733876088121-0.0003923624806380.013549805313-0.3912474408430.1997057112570.01464581180170.499716643508-0.00711022649001-0.03905984909570.44396310032-0.02179371055690.28729348496-83.54124.99710.328
50.896308739760.685504992657-0.02166831228491.644415017610.07134021345542.112413045310.0133585440531-0.0865781972943-0.1376032071020.106076657044-0.0514233429324-0.09577142438680.41102172620.1527426226620.02072767484590.5131828409710.08718170365830.020830661930.436495373554-0.01387687470830.288583024402-80.241-14.0287.088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 608:608 )A608
2X-RAY DIFFRACTION2( CHAIN A AND RESID 3:115 )A3 - 115
3X-RAY DIFFRACTION3( CHAIN A AND RESID 116:169 )A116 - 169
4X-RAY DIFFRACTION4( CHAIN A AND RESID 170:341 )A170 - 341
5X-RAY DIFFRACTION5( CHAIN A AND RESID 342:548 )A342 - 548

+
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