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- PDB-8ie2: Crystal structure of Lactiplantibacillus plantarum GlyRS -

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Basic information

Entry
Database: PDB / ID: 8ie2
TitleCrystal structure of Lactiplantibacillus plantarum GlyRS
Components
  • Glycine--tRNA ligase alpha subunit
  • Glycine--tRNA ligase beta subunit
KeywordsTRANSFERASE / LIGASE / aminoacyl-tRNA synthetase
Function / homology
Function and homology information


glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / transferase activity / ATP binding / cytoplasm
Similarity search - Function
Glycine-tRNA ligase, beta subunit / Glycyl-tRNA synthetase beta subunit / Glycine-tRNA ligase, alpha subunit / Glycine-tRNA synthetase, heterodimeric / Glycyl-tRNA synthetase alpha subunit / Heterodimeric glycyl-transfer RNA synthetases family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
Glycine--tRNA ligase alpha subunit / Glycine--tRNA ligase beta subunit
Similarity search - Component
Biological speciesLactiplantibacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsYamashita, S. / Tomita, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03980 Japan
Japan Society for the Promotion of Science (JSPS)19K16053 Japan
CitationJournal: J.Biochem. / Year: 2023
Title: Mechanism of tRNA recognition by heterotetrameric glycyl-tRNA synthetase from lactic acid bacteria.
Authors: Nagato, Y. / Yamashita, S. / Ohashi, A. / Furukawa, H. / Takai, K. / Tomita, K. / Tomikawa, C.
History
DepositionFeb 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glycine--tRNA ligase alpha subunit
A: Glycine--tRNA ligase alpha subunit
D: Glycine--tRNA ligase alpha subunit
C: Glycine--tRNA ligase alpha subunit
H: Glycine--tRNA ligase beta subunit
F: Glycine--tRNA ligase beta subunit
E: Glycine--tRNA ligase beta subunit
G: Glycine--tRNA ligase beta subunit


Theoretical massNumber of molelcules
Total (without water)453,4508
Polymers453,4508
Non-polymers00
Water0
1
B: Glycine--tRNA ligase alpha subunit
A: Glycine--tRNA ligase alpha subunit
F: Glycine--tRNA ligase beta subunit
E: Glycine--tRNA ligase beta subunit


Theoretical massNumber of molelcules
Total (without water)226,7254
Polymers226,7254
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Glycine--tRNA ligase alpha subunit
C: Glycine--tRNA ligase alpha subunit
H: Glycine--tRNA ligase beta subunit
G: Glycine--tRNA ligase beta subunit


Theoretical massNumber of molelcules
Total (without water)226,7254
Polymers226,7254
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.140, 163.170, 155.280
Angle α, β, γ (deg.)90.00, 119.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycine--tRNA ligase alpha subunit / Glycyl-tRNA synthetase alpha subunit / GlyRS


Mass: 34729.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The N-terminal GlyPro is derived from expression vector. (Rest of the HRV3c cleavage site)
Source: (gene. exp.) Lactiplantibacillus plantarum WCFS1 (bacteria)
Strain: WCFS1 / Gene: glyQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q88VS2, glycine-tRNA ligase
#2: Protein
Glycine--tRNA ligase beta subunit / Glycyl-tRNA synthetase beta subunit / GlyRS


Mass: 78633.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum WCFS1 (bacteria)
Strain: WCFS1 / Gene: glyS / Production host: Escherichia coli (E. coli) / References: UniProt: Q88VS3, glycine-tRNA ligase

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12% PEG3350, 4% Tacsimate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 46387 / % possible obs: 59.5 % / Redundancy: 6.8 % / CC1/2: 0.989 / Rmerge(I) obs: 0.258 / Rrim(I) all: 0.279 / Net I/σ(I): 6.82
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.6-3.690.6786910.7460.7351
3.69-3.80.68811800.7390.7431
3.8-3.910.64515150.8280.6971
3.91-4.030.60517840.8510.6541
4.03-4.160.5620310.8830.6051
4.16-4.30.50123070.920.5411
4.3-4.470.42224660.940.4571
4.47-4.650.39326670.9430.4261
4.65-4.850.40328690.940.4371
4.85-5.090.42929620.930.4681
5.09-5.370.46531760.930.5031
5.37-5.690.52532410.9150.5641
5.69-6.090.52734500.9170.5671
6.09-6.570.45433340.9340.4881
6.57-7.20.29830220.9650.321
7.2-8.050.16627860.9890.1791
8.05-9.30.09924350.9940.1071
9.3-11.390.06620520.9960.0731
11.39-16.10.06316000.9970.0681
16.1-500.0628190.9970.0681

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→48.63 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: TWIN_LSQ_F
Details: The anisotropically scaled and truncated mtz file were used for the final refinement.
RfactorNum. reflection% reflection
Rfree0.2442 2383 5.14 %
Rwork0.2153 --
obs0.2217 46387 59.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30972 0 0 0 30972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431608
X-RAY DIFFRACTIONf_angle_d0.85242738
X-RAY DIFFRACTIONf_dihedral_angle_d22.55211838
X-RAY DIFFRACTIONf_chiral_restr0.0514696
X-RAY DIFFRACTIONf_plane_restr0.0065576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.670.324240.2926436X-RAY DIFFRACTION10
3.67-3.750.3492530.2779792X-RAY DIFFRACTION17
3.75-3.840.2871560.27691098X-RAY DIFFRACTION24
3.84-3.940.2495560.25681314X-RAY DIFFRACTION29
3.94-4.040.2986620.24461544X-RAY DIFFRACTION34
4.04-4.160.2662940.241763X-RAY DIFFRACTION38
4.16-4.30.29881150.24052003X-RAY DIFFRACTION44
4.3-4.450.26361030.22742230X-RAY DIFFRACTION49
4.45-4.630.23081430.21942487X-RAY DIFFRACTION54
4.63-4.840.26081420.20892766X-RAY DIFFRACTION61
4.84-5.090.27511790.20733033X-RAY DIFFRACTION66
5.09-5.410.25631660.22213451X-RAY DIFFRACTION75
5.41-5.830.29461970.22383878X-RAY DIFFRACTION85
5.83-6.410.25882380.23184305X-RAY DIFFRACTION93
6.42-7.340.23032320.21494301X-RAY DIFFRACTION94
7.34-9.240.21352340.19334336X-RAY DIFFRACTION94
9.24-48.630.21052530.2114303X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.4135-0.4522-0.10310.87350.56021.43730.21610.1528-0.0845-0.2080.0156-0.14690.41780.0333-0.2080.4785-0.02570.00260.3994-0.08080.25742.707-3.45133.279
21.8442-0.3938-0.30650.629-0.62571.61630.21490.1539-0.1319-0.06350.0102-0.08190.18570.1806-0.20740.2473-0.0522-0.10240.2083-0.09320.25838.7080.28655.439
31.69440.24430.15531.31010.26741.8067-0.11970.14540.23950.16410.1131-0.3998-0.0287-0.0631-0.0040.3759-0.0638-0.14980.2753-0.01660.4715-4.738-66.41357.582
41.22410.3267-0.10331.5425-0.17281.8171-0.03230.03710.1831-0.0729-0.1107-0.1739-0.0035-0.01670.12350.08140.00550.01170.35240.07710.4079-20.921-70.03941.273
50.63680.0016-0.663-0.00010.05092.97880.2299-0.3721-0.3591-0.73220.30890.50770.8620.4618-0.51910.709-0.0826-0.32440.63-0.15650.9125-25.394-5.8679.96
60.2554-0.4491-0.50891.02980.5291.53450.71390.619-0.2062-0.12880.6804-0.8501-0.9291-0.0131-0.97651.1818-0.0286-0.21320.9331-0.12510.8593-50.789-31.975-16.892
71.3850.26910.47010.3810.36790.4940.0219-0.0731-0.1963-0.2944-0.01160.0757-0.34280.0973-0.03190.5333-0.21860.14270.45360.08860.42070.48915.8437.191
82.60050.1176-0.16042.04710.31312.50330.0712-0.1279-0.71670.10090.25580.28840.6888-0.3966-0.16850.6961-0.04610.21540.65750.10230.579322.396-9.207-3.684
90.80890.79310.350.76910.34650.15-0.00340.0166-0.42840.16310.22960.18081.3316-0.6966-0.19591.442-0.3046-0.04820.7580.23241.259714.975-32.327-33.322
101.3423-0.52720.31630.6526-0.47331.2307-0.05380.08360.50050.3443-0.23740.0888-0.48880.36830.19890.2837-0.19080.02670.3389-0.19060.51438.11624.83282.819
110.90530.0553-0.23850.05390.04050.12250.207-0.1387-0.2330.2988-0.0526-0.23950.1472-0.0601-0.04861.4237-0.83740.16331.2872-0.21710.655719.88240.55591.766
121.7254-0.35461.23961.3123-0.81871.78880.14940.292-0.587-0.28720.22680.0660.3850.01330.0494-0.008-0.23740.04080.5157-0.01170.2542-5.585-5.92183.728
132.14460.3317-0.54961.9467-0.77981.64040.3219-0.4043-0.76770.2543-0.2694-0.6768-0.07570.3263-0.03660.63340.1452-0.27350.4907-0.14810.82724.876-21.4886.63
141.18250.19880.70530.741-0.4510.85110.2430.1814-0.2815-0.4978-0.0497-0.0379-0.2560.2669-0.1250.7961-0.168-0.00590.5216-0.24860.801549.075-11.392114.52
150.86330.97770.65412.4631.19610.6474-0.0845-0.84110.09870.3862-0.45620.2384-0.1086-1.01170.58350.82680.0129-0.15080.9916-0.19030.76581.357-63.76493.701
160.25180.05120.15390.6594-0.36710.85050.0984-0.0236-0.16510.28490.0645-0.19570.3910.1877-0.20981.47620.4663-0.58180.7017-0.29420.8253.046-49.733110.519
170.44110.2817-0.49780.37360.051.4111-0.1033-0.2969-0.0670.2372-0.3046-0.10410.51860.0930.26950.428-0.0124-0.13910.490.18590.614916.683-85.28572.319
181.95950.677-0.21282.26770.21631.24760.0726-0.26590.8984-0.0244-0.08240.4772-0.4173-0.139-0.09420.22570.03830.12790.44830.16110.629337.419-60.30459.171
190.2615-0.07970.33520.8824-1.40782.46210.10270.1944-0.12120.7961-0.2153-0.0847-0.29650.3778-0.04560.87010.19560.10130.4943-0.21130.882159.68-38.03980.983
202.1019-0.3457-0.0161.6348-0.85512.7803-0.14130.2086-0.4253-0.0640.4536-0.04090.57130.1967-0.16650.2291-0.04520.05740.4278-0.14110.3991-44.979-94.65528.321
210.3930.0188-0.11880.04290.16190.66280.5496-0.1539-0.3568-0.1048-0.26310.37350.95640.0883-0.38161.8259-0.2082-0.39750.6151-0.0331.3914-43.764-123.95-2.33
220.7542-0.2117-0.42031.66480.21111.54820.0528-0.06530.2-0.0539-0.0976-0.0734-0.30150.0367-0.03880.01790.0210.04910.29160.07140.1854-52.52-63.79939.853
231.7273-0.20360.18710.3908-0.29591.70420.14510.41930.0286-0.02-0.1104-0.170.13060.2281-0.04390.43520.0460.07780.31790.01580.3824-40.901-48.36311.744
240.29-0.2574-0.14120.6695-0.72571.65330.19220.2838-0.0719-0.25030.05020.40220.7608-0.0502-0.15710.9513-0.1052-0.14740.556-0.04760.6795-52.693-58.901-22.441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:299 )A1 - 299
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:299 )B1 - 299
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:299 )C1 - 299
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:299 )D1 - 299
5X-RAY DIFFRACTION5( CHAIN E AND ( RESID 1:63 OR RESID 125:212 ) )E1 - 63
6X-RAY DIFFRACTION5( CHAIN E AND ( RESID 1:63 OR RESID 125:212 ) )E125 - 212
7X-RAY DIFFRACTION6( CHAIN E AND RESID 64:124 )E64 - 124
8X-RAY DIFFRACTION7( CHAIN E AND RESID 213:337 )E213 - 337
9X-RAY DIFFRACTION8( CHAIN E AND RESID 338:545 )E338 - 545
10X-RAY DIFFRACTION9( CHAIN E AND RESID 546:694 )E546 - 694
11X-RAY DIFFRACTION10( CHAIN F AND ( RESID 1:63 OR RESID 125:212 ) )F1 - 63
12X-RAY DIFFRACTION10( CHAIN F AND ( RESID 1:63 OR RESID 125:212 ) )F125 - 212
13X-RAY DIFFRACTION11( CHAIN F AND RESID 64:124 )F64 - 124
14X-RAY DIFFRACTION12( CHAIN F AND RESID 213:337 )F213 - 337
15X-RAY DIFFRACTION13( CHAIN F AND RESID 338:545 )F338 - 545
16X-RAY DIFFRACTION14( CHAIN F AND RESID 546:694 )F546 - 694
17X-RAY DIFFRACTION15( CHAIN G AND ( RESID 1:63 OR RESID 125:212 ) )G1 - 63
18X-RAY DIFFRACTION15( CHAIN G AND ( RESID 1:63 OR RESID 125:212 ) )G125 - 212
19X-RAY DIFFRACTION16( CHAIN G AND RESID 64:124 )G64 - 124
20X-RAY DIFFRACTION17( CHAIN G AND RESID 213:337 )G213 - 337
21X-RAY DIFFRACTION18( CHAIN G AND RESID 338:545 )G338 - 545
22X-RAY DIFFRACTION19( CHAIN G AND RESID 546:694 )G546 - 694
23X-RAY DIFFRACTION20( CHAIN H AND ( RESID 1:63 OR RESID 125:212 ) )H1 - 63
24X-RAY DIFFRACTION20( CHAIN H AND ( RESID 1:63 OR RESID 125:212 ) )H125 - 212
25X-RAY DIFFRACTION21( CHAIN H AND RESID 64:124 )H64 - 124
26X-RAY DIFFRACTION22( CHAIN H AND RESID 213:337 )H213 - 337
27X-RAY DIFFRACTION23( CHAIN H AND RESID 338:545 )H338 - 545
28X-RAY DIFFRACTION24( CHAIN H AND RESID 546:694 )H546 - 694

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