[English] 日本語
Yorodumi
- PDB-8slg: Crystal Structure of Glycine tRNA ligase from Mycobacterium therm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8slg
TitleCrystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (glycyl adenylate bound)
ComponentsGlycine--tRNA ligase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Glycine-tRNA ligase, bacterial / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II ...Glycine-tRNA ligase, bacterial / Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-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)
Similarity search - Domain/homology
5'-O-(glycylsulfamoyl)adenosine / Glycine--tRNA ligase
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (glycyl adenylate bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Seibold, S.
History
DepositionApr 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycine--tRNA ligase
B: Glycine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,42411
Polymers110,1612
Non-polymers1,2629
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-40 kcal/mol
Surface area33950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.248, 87.108, 99.358
Angle α, β, γ (deg.)90.00, 104.21, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glycine--tRNA ligase


Mass: 55080.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Gene: glyQS / Plasmid: MythA.19107.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7CIG9

-
Non-polymers , 5 types, 298 molecules

#2: Chemical ChemComp-G5A / 5'-O-(glycylsulfamoyl)adenosine


Mass: 403.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Index F11: 0.2M NaCl, 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG3350, MythA.19107.a.A1.PW39162 at 17 mg/mL. Plate:13141 well F11 drop 1. Puck: PSL-0705, Cryo: 15% Glycerol + 85% Crystallant. 2mM 5'- ...Details: Index F11: 0.2M NaCl, 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG3350, MythA.19107.a.A1.PW39162 at 17 mg/mL. Plate:13141 well F11 drop 1. Puck: PSL-0705, Cryo: 15% Glycerol + 85% Crystallant. 2mM 5'-O-(glycylsulfamoyl)adenosine (G5A) added prior to crystallization.
PH range: '

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→96.32 Å / Num. obs: 102442 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Χ2: 1.01 / Net I/σ(I): 13 / Num. measured all: 710881
Reflection shellResolution: 1.95→2 Å / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.072 / Num. measured all: 49368 / Num. unique obs: 7532 / CC1/2: 0.829 / Rpim(I) all: 0.453 / Rrim(I) all: 1.166 / Χ2: 1.05 / Net I/σ(I) obs: 1.6

-
Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4932: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.16 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 5091 4.98 %
Rwork0.1743 --
obs0.1756 102260 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7072 0 76 289 7437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077325
X-RAY DIFFRACTIONf_angle_d0.9429952
X-RAY DIFFRACTIONf_dihedral_angle_d13.9192667
X-RAY DIFFRACTIONf_chiral_restr0.0511054
X-RAY DIFFRACTIONf_plane_restr0.0121299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.34341920.29533165X-RAY DIFFRACTION100
1.97-20.30761730.27243236X-RAY DIFFRACTION100
2-2.020.30551570.2573176X-RAY DIFFRACTION99
2.02-2.050.25551830.22873208X-RAY DIFFRACTION100
2.05-2.070.22571760.21443273X-RAY DIFFRACTION100
2.07-2.10.22671510.20253175X-RAY DIFFRACTION100
2.1-2.130.23051610.19743276X-RAY DIFFRACTION100
2.13-2.160.22561660.19263186X-RAY DIFFRACTION99
2.16-2.20.22421570.19133235X-RAY DIFFRACTION100
2.2-2.230.22391550.1863255X-RAY DIFFRACTION100
2.23-2.270.21031590.18453241X-RAY DIFFRACTION100
2.27-2.310.2011580.18713244X-RAY DIFFRACTION100
2.31-2.360.20881760.18323226X-RAY DIFFRACTION100
2.36-2.40.23751590.18793222X-RAY DIFFRACTION100
2.4-2.460.26021790.18583220X-RAY DIFFRACTION100
2.46-2.510.21131900.18763229X-RAY DIFFRACTION100
2.51-2.580.24591740.17643204X-RAY DIFFRACTION100
2.58-2.650.231620.18193304X-RAY DIFFRACTION100
2.65-2.720.21881700.18093203X-RAY DIFFRACTION100
2.72-2.810.23211780.18393257X-RAY DIFFRACTION100
2.81-2.910.20081550.18963249X-RAY DIFFRACTION100
2.91-3.030.22661740.18983218X-RAY DIFFRACTION100
3.03-3.170.20551790.19343254X-RAY DIFFRACTION100
3.17-3.330.22951730.18653250X-RAY DIFFRACTION100
3.33-3.540.21131760.18413255X-RAY DIFFRACTION100
3.54-3.820.19561790.16873250X-RAY DIFFRACTION100
3.82-4.20.15191600.14223252X-RAY DIFFRACTION100
4.2-4.810.12851740.12673275X-RAY DIFFRACTION100
4.81-6.050.17381780.15563282X-RAY DIFFRACTION100
6.06-48.160.22371670.17983349X-RAY DIFFRACTION99
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)
11.5713-0.24841.03321.6882-0.9162.9906-0.020.097-0.1853-0.10490.0317-0.07880.28850.0162-0.0310.341-0.05040.06360.2932-0.02330.2897-20.12736.912513.1093
21.2727-2.12490.8577.2377-1.92013.0023-0.16630.2506-0.6496-0.9755-0.9003-1.09481.77290.21620.25851.3750.08740.11990.63620.06821.288-26.287411.41982.548
31.8363-0.15380.70270.5183-0.05751.79860.02440.2796-0.1037-0.1907-0.00220.06460.12150.06420.00480.4217-0.0691-0.00740.365-0.01680.3205-23.920240.4249-0.9
41.52990.18271.36170.82720.71114.1366-0.0515-0.07210.01720.1110.0097-0.07080.21180.30040.04950.3271-0.050.04550.40020.0360.3418-7.607143.006624.5775
51.7573-0.11571.05193.4652-0.75034.4491-0.08950.01570.1830.12920.0193-0.08-0.15910.31040.08020.2885-0.04470.01630.48960.00040.3788-1.042548.812532.565
61.0093-0.26230.85692.0664-0.69692.9218-0.097-0.04380.0756-0.11070.00020.1761-0.0886-0.29530.06640.2504-0.02730.01230.3717-0.00460.3247-33.255950.700216.8254
79.1733-1.97692.91151.7155-0.00975.8437-0.322-0.82730.310.015-0.10690.3157-0.5224-1.36110.42430.5732-0.101-0.02210.7612-0.06610.5764-55.502834.479120.7437
80.70190.02660.24781.2388-0.36651.7078-0.0162-0.2274-0.0490.05830.05380.21280.0828-0.4359-0.04930.3137-0.04970.02880.51760.00950.359-35.302442.701431.192
91.78850.11310.28031.87270.09762.3432-0.24550.24260.3417-0.06160.1372-0.243-0.39420.03490.18730.5416-0.0122-0.1190.36320.01440.5629-21.980872.923211.0647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -19 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 318 )
4X-RAY DIFFRACTION4chain 'A' and (resid 319 through 392 )
5X-RAY DIFFRACTION5chain 'A' and (resid 393 through 461 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 70 )
7X-RAY DIFFRACTION7chain 'B' and (resid 71 through 147 )
8X-RAY DIFFRACTION8chain 'B' and (resid 148 through 345 )
9X-RAY DIFFRACTION9chain 'B' and (resid 346 through 461 )

+
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