[English] 日本語
Yorodumi
- PDB-9l8v: PyrN C-terminl domain in complex with L-glutamyl-sulfamoyl-adenos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9l8v
TitlePyrN C-terminl domain in complex with L-glutamyl-sulfamoyl-adenosine (GSA)
ComponentsMethionine-tRNA ligase
KeywordsLIGASE / Methionine Biosynthesis Streptomyces ATP
Function / homology
Function and homology information


methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP binding / cytosol
Similarity search - Function
Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Cupin 2, conserved barrel / Cupin domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / RmlC-like cupin domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / RmlC-like jelly roll fold
Similarity search - Domain/homology
O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE / Methionine-tRNA ligase
Similarity search - Component
Biological speciesStreptomyces candidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsDu, Y.L. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: PyrN C-terminl domain in complex with L-glutamyl-sulfamoyl-adenosine (GSA)
Authors: Du, Y.L. / Du, Y.L.
History
DepositionDec 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methionine-tRNA ligase
B: Methionine-tRNA ligase
D: Methionine-tRNA ligase
B00Z: Methionine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,60824
Polymers238,6214
Non-polymers3,98720
Water16,232901
1
A: Methionine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4575
Polymers59,6551
Non-polymers8014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8477
Polymers59,6551
Non-polymers1,1926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Methionine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6526
Polymers59,6551
Non-polymers9975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B00Z: Methionine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6526
Polymers59,6551
Non-polymers9975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.010, 243.810, 100.620
Angle α, β, γ (deg.)90.000, 99.040, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 12 through 70 or (resid 71...
d_2ens_1(chain "B" and (resid 12 through 70 or (resid 71...
d_3ens_1(chain "C" and (resid 12 through 70 or (resid 71...
d_4ens_1(chain "D" and (resid 12 through 129 or (resid 130...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGPROPROAA12 - 5429 - 539
d_12MESMESMESMESAE601
d_21ARGARGPROPROBB12 - 5429 - 539
d_22MESMESMESMESBK603
d_31ARGARGPROPROB00ZD12 - 5429 - 539
d_32MESMESMESMESB00ZT601
d_41ARGARGPROPRODC12 - 5429 - 539
d_42MESMESMESMESDO601

NCS oper:
IDCodeMatrixVector
1given(0.593764309652, 0.00185468673955, 0.804636877555), (0.0239605355366, -0.999594636717, -0.0153770927847), (0.804282187619, 0.0284098993805, -0.59356805869)-3.44133768013, 46.6521086925, 5.86295107031
2given(-0.99854858881, 0.0170585816213, 0.0510854243187), (0.0398737199533, 0.871767522354, 0.48829445361), (-0.0362050029946, 0.489622703479, -0.871182418324)31.7259066867, -55.5867223795, -53.5485542104
3given(-0.499800708469, -0.00169090991032, -0.866138783705), (0.429088292886, -0.869145170164, -0.245906303476), (-0.752384535143, -0.494554156796, 0.435124921457)36.0913734369, -11.8091687694, -35.9656272739

-
Components

#1: Protein
Methionine-tRNA ligase / PyfG / PyrN


Mass: 59655.262 Da / Num. of mol.: 4 / Fragment: C-terminl domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces candidus (bacteria) / Gene: pyrN, prfJ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A516ELE7
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GSU / O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE


Type: L-peptide linking / Mass: 475.434 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H21N7O9S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: 13% PEG20000; 0.1M MES; 4% 1,3-Butanediol; 15% Ethylene Glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.23→33.12 Å / Num. obs: 115139 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 33.63 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.5
Reflection shellResolution: 2.23→2.31 Å / Num. unique obs: 11464 / CC1/2: 0.627

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→33.12 Å / SU ML: 0.253 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 1999 1.74 %
Rwork0.1872 113125 -
obs0.188 115124 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.24 Å2
Refinement stepCycle: LAST / Resolution: 2.23→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16365 0 232 901 17498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008417029
X-RAY DIFFRACTIONf_angle_d1.00323210
X-RAY DIFFRACTIONf_chiral_restr0.05312498
X-RAY DIFFRACTIONf_plane_restr0.00943079
X-RAY DIFFRACTIONf_dihedral_angle_d16.1476130
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.787230982714
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS2.05873724708
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS2.15743310201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.290.30211440.26978145X-RAY DIFFRACTION99.95
2.29-2.350.28031410.24668001X-RAY DIFFRACTION99.96
2.35-2.420.26351430.23078045X-RAY DIFFRACTION99.99
2.42-2.490.31571430.22948115X-RAY DIFFRACTION99.99
2.49-2.580.25821420.21958016X-RAY DIFFRACTION99.99
2.58-2.690.2521430.21318094X-RAY DIFFRACTION100
2.69-2.810.28411430.20928073X-RAY DIFFRACTION99.99
2.81-2.960.29691430.20548095X-RAY DIFFRACTION100
2.96-3.140.24711420.1968088X-RAY DIFFRACTION99.99
3.14-3.380.21431430.19068049X-RAY DIFFRACTION99.95
3.38-3.730.22781430.17548077X-RAY DIFFRACTION99.99
3.73-4.260.22371420.16418102X-RAY DIFFRACTION99.98
4.26-5.370.20691440.15548099X-RAY DIFFRACTION99.99
5.37-33.120.19331430.16288126X-RAY DIFFRACTION99.59
Refinement TLS params.Method: refined / Origin x: 16.2285387223 Å / Origin y: -3.99577531865 Å / Origin z: -21.0619630866 Å
111213212223313233
T0.218518952076 Å20.0220051965304 Å2-0.0222328831328 Å2-0.263837202192 Å2-0.00691624197416 Å2--0.25116479784 Å2
L0.0344267660045 °2-0.113247918003 °2-0.086424494708 °2-0.402831228117 °20.270893199465 °2--0.200190598277 °2
S0.00472603939897 Å °0.00676961622311 Å °-0.00639920475477 Å °-0.0161341159498 Å °0.00496165124904 Å °-0.00317044072903 Å °-0.0246358321981 Å °0.00392444852083 Å °-0.00875524241517 Å °
Refinement TLS groupSelection details: all

+
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