[English] 日本語
Yorodumi
- PDB-7k9m: Crystal structure of the complex of M. tuberculosis PheRS with co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k9m
TitleCrystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and 5'-O-(N-phenylalanyl)sulfamoyl-adenosine
Components
  • (Phenylalanine--tRNA ligase ...) x 2
  • tRNA(Phe)
KeywordsLIGASE/RNA / aminoacylation / phenylalanyl tRNA synthetase / adenylate analog / LIGASE-RNA complex / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / peptidoglycan-based cell wall / tRNA binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain ...Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/4 domain / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Putative DNA-binding domain superfamily / 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, OB-fold
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / 5'-O-(L-phenylalanylsulfamoyl)adenosine / : / RNA / RNA (> 10) / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMichalska, K. / Chang, C. / Jedrzejczak, R. / Wower, J. / Baragana, B. / Forte, B. / Gilbert, I.H. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation.
Authors: Michalska, K. / Jedrzejczak, R. / Wower, J. / Chang, C. / Baragana, B. / Gilbert, I.H. / Forte, B. / Joachimiak, A.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 16, 2021Group: Database references / Category: pdbx_database_related
Revision 1.3Oct 18, 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: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
C: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,76916
Polymers151,1253
Non-polymers1,64413
Water5,801322
1
A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
C: tRNA(Phe)
hetero molecules

A: Phenylalanine--tRNA ligase alpha subunit
B: Phenylalanine--tRNA ligase beta subunit
C: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,53832
Polymers302,2516
Non-polymers3,28726
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area35210 Å2
ΔGint-187 kcal/mol
Surface area112620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.432, 110.753, 147.897
Angle α, β, γ (deg.)90.000, 103.590, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Phenylalanine--tRNA ligase ... , 2 types, 2 molecules AB

#1: Protein Phenylalanine--tRNA ligase alpha subunit / Phenylalanyl-tRNA synthetase alpha subunit / PheRS


Mass: 37415.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pheS, Rv1649, MTCY06H11.14 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: P9WFU3, phenylalanine-tRNA ligase
#2: Protein Phenylalanine--tRNA ligase beta subunit / Phenylalanyl-tRNA synthetase beta subunit / PheRS


Mass: 88867.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pheT, Rv1650, MTCY06H11.15 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: P9WFU1, phenylalanine-tRNA ligase

-
RNA chain , 1 types, 1 molecules C

#3: RNA chain tRNA(Phe)


Mass: 24842.811 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
References: GenBank: 1251771558

-
Non-polymers , 6 types, 335 molecules

#4: Chemical ChemComp-W5Y / 5'-O-(L-phenylalanylsulfamoyl)adenosine


Mass: 493.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O7S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium sodium tartrate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 68621 / % possible obs: 99 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.073 / Rrim(I) all: 0.186 / Χ2: 0.935 / Net I/σ(I): 5.5 / Num. measured all: 427793
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.90.83232740.5220.4650.9590.95496.2
2.54-2.594.30.80433750.5740.4280.9160.93797.2
2.59-2.645.10.80134620.6220.3930.8960.93999.6
2.64-2.695.50.75133980.6710.3580.8340.94999.6
2.69-2.755.90.71934480.7180.3280.7920.93999.7
2.75-2.826.20.66634550.7820.2930.7290.96299.7
2.82-2.896.40.59434000.8370.2560.6480.96599.7
2.89-2.966.50.55134640.8680.2340.60.97399.6
2.96-3.056.50.45434180.9160.1910.4940.98198.7
3.05-3.1560.38233620.9360.1640.417197.1
3.15-3.266.90.31434360.9550.1280.340.98899.5
3.26-3.3970.25234690.9730.1030.2730.99299.7
3.39-3.556.90.19634440.9790.0810.2121.00299.9
3.55-3.736.90.15734410.9860.0640.171.00399.6
3.73-3.976.70.12434490.9890.0510.1350.97399.3
3.97-4.276.40.09634130.9930.040.1040.94898
4.27-4.77.10.0834790.9950.0320.0860.92699.9
4.7-5.3870.07534530.9950.030.0810.84599.2
5.38-6.786.50.0734360.9950.0290.0760.74498.4
6.78-506.80.04435450.9980.0180.0480.7199.2

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
SBC-Collectdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7KA0

7ka0


Resolution: 2.5→47.92 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 3264 4.9 %
Rwork0.1793 63320 -
obs0.181 66584 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.21 Å2 / Biso mean: 56.7561 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: final / Resolution: 2.5→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8861 1413 108 322 10704
Biso mean--54.38 36.99 -
Num. residues----1239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.540.33681110.26362087219874
2.54-2.580.27611270.23962317244481
2.58-2.620.30821210.23232473259487
2.62-2.670.25521390.21662619275891
2.67-2.720.25221250.21182719284495
2.72-2.770.26061580.21322755291397
2.77-2.830.24751540.21772835298998
2.83-2.890.25211480.2222769291799
2.89-2.950.26661400.22052881302199
2.95-3.030.26731290.21472832296198
3.03-3.110.27031560.21092755291197
3.11-3.20.23091410.2082805294698
3.2-3.30.22031580.20832841299999
3.3-3.420.24331550.20328553010100
3.42-3.560.22231250.187628893014100
3.56-3.720.21441500.171428513001100
3.72-3.920.18081470.16352847299499
3.92-4.160.16281650.14962796296198
4.16-4.480.17631450.137728833028100
4.48-4.930.18171470.130328743021100
4.93-5.650.17941410.15132864300599
5.65-7.110.20661180.16752888300698
7.11-47.920.18311640.15632885304998
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)
10.9050.29250.76080.8590.90022.73270.44380.4991-0.36980.1306-0.1221-0.36871.177-0.3554-0.26140.9655-0.0082-0.27650.8534-0.16720.9201-69.8014-1.5458109.2149
20.2655-0.0787-0.13880.0441-0.0660.62810.00470.2921-0.1881-0.23450.10140.01140.2404-0.1578-0.03770.4207-0.1299-0.05880.4423-0.01730.3881-63.065713.9604123.068
30.61340.3019-0.09471.01280.13750.58830.0591-0.04310.02610.0854-0.045-0.0368-0.07610.01670.00030.1767-0.02960.02340.2153-0.01510.223-26.216763.2433162.7776
40.69950.0379-0.23390.6394-0.77091.2054-0.0318-0.2722-0.22880.36590.16070.0102-0.1054-0.2579-0.12570.70810.02610.070.50420.05780.3932-35.968765.2452207.3485
50.3811-0.4105-0.17880.57510.33381.389-0.1326-0.24620.07870.5320.1361-0.2757-0.11640.1104-0.00080.67720.0225-0.04490.3744-0.06850.3523-22.135980.3748195.7379
60.99350.1137-0.07610.98850.33841.3254-0.0657-0.31590.09190.57570.0736-0.306-0.16020.27580.0050.6219-0.0041-0.11110.3847-0.08970.384-13.844580.5271189.7521
70.2752-0.01260.01860.63680.26470.4260.0870.0069-0.0642-0.0172-0.0637-0.13820.03290.0329-0.03040.15870.00730.01860.21660.00610.2527-18.14236.0242145.0669
81.90720.33621.54370.5460.74161.70960.23380.01340.0630.5-0.0029-0.3525-0.22840.2054-0.31321.22230.0091-0.16751.35760.0580.9268-53.416518.442297.2116
90.51010.0462-0.28370.0264-0.0210.1591-0.59990.4142-0.5272-0.1048-0.27390.02930.23470.0680.7061.679-0.1276-0.6541.7884-0.03341.3461-52.62037.907799.641
100.19740.37210.42090.71320.81120.92351.11490.9046-1.4416-0.83810.03430.93280.963-0.5243-0.81091.00510.1007-0.51721.1882-0.08651.1117-38.23238.4026115.5243
110.2952-0.73370.23362.68050.79213.1728-0.2572-1.17620.8242-0.0238-0.2442-0.1684-0.4991-0.79750.43031.28010.0895-0.19071.3345-0.08611.1248-66.901624.328296.5875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 52 )A3 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 110 )A53 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 341 )A111 - 341
4X-RAY DIFFRACTION4chain 'B' and (resid -3 through 131 )B-3 - 131
5X-RAY DIFFRACTION5chain 'B' and (resid 132 through 231 )B132 - 231
6X-RAY DIFFRACTION6chain 'B' and (resid 232 through 486 )B232 - 486
7X-RAY DIFFRACTION7chain 'B' and (resid 487 through 831 )B487 - 831
8X-RAY DIFFRACTION8chain 'C' and (resid 5 through 19 )C5 - 19
9X-RAY DIFFRACTION9chain 'C' and (resid 20 through 24 )C20 - 24
10X-RAY DIFFRACTION10chain 'C' and (resid 25 through 49 )C25 - 49
11X-RAY DIFFRACTION11chain 'C' and (resid 50 through 70 )C50 - 70

+
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