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- PDB-4gri: Crystal structure of a glutamyl-tRNA synthetase GluRS from Borrel... -

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Basic information

Entry
Database: PDB / ID: 4gri
TitleCrystal structure of a glutamyl-tRNA synthetase GluRS from Borrelia burgdorferi bound to glutamic acid and zinc
ComponentsGlutamate--tRNA ligase
KeywordsLIGASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / aminoacyl-tRNA synthetase / ATP-dependent / transferase / aaRS / GluRS / tRNAglu
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 / Glutamate-tRNA synthetase, class I, anticodon-binding domain, subdomain 1 / Arc Repressor Mutant, subunit A - #350 / Glutamate-tRNA ligase, bacterial/mitochondrial / Glutamyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon binding domain / : ...Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 / Glutamate-tRNA synthetase, class I, anticodon-binding domain, subdomain 1 / Arc Repressor Mutant, subunit A - #350 / Glutamate-tRNA ligase, bacterial/mitochondrial / Glutamyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon binding domain / : / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / HUPs / Helicase, Ruva Protein; domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Glutamate--tRNA ligase
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2017
Title: Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms.
Authors: Moen, S.O. / Edwards, T.E. / Dranow, D.M. / Clifton, M.C. / Sankaran, B. / Van Voorhis, W.C. / Sharma, A. / Manoil, C. / Staker, B.L. / Myler, P.J. / Lorimer, D.D.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)118,9317
Polymers118,4702
Non-polymers4615
Water5,206289
1
A: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4834
Polymers59,2351
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4483
Polymers59,2351
Non-polymers2132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.460, 110.310, 197.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate--tRNA ligase / Glutamyl-tRNA synthetase / GluRS


Mass: 59235.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_0372, gltX / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: O51345, glutamate-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: BobuA.01348.a.A1 at 28 mg/mL with 20 mM glutamic acid against Wiz3 screen condition A8, 20% PEG 3350, 0.2 M KNO3 with 15% ethylene glycol as cryo-protectant, crystal tracking ID 233969a8, ...Details: BobuA.01348.a.A1 at 28 mg/mL with 20 mM glutamic acid against Wiz3 screen condition A8, 20% PEG 3350, 0.2 M KNO3 with 15% ethylene glycol as cryo-protectant, crystal tracking ID 233969a8, unique puck ID qax1-1, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 42317 / Num. obs: 41054 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 39.822 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.6-2.670.3743.3911525276288.9
2.67-2.740.3553.5211651276992.8
2.74-2.820.2834.1112128277695.1
2.82-2.910.2534.5812587277897
2.91-30.2175.2412693270598.4
3-3.110.197612840260498
3.11-3.220.186.8813334252397.3
3.22-3.360.158.3913403241797.3
3.36-3.510.13111.0812850232397.4
3.51-3.680.11312.7312717225798.4
3.68-3.880.10214.0212415215198.9
3.88-4.110.09215.5312389207198.6
4.11-4.390.08317.0511997192299
4.39-4.750.07718.1711095179798.8
4.75-5.20.08117.5910559168299.4
5.2-5.810.08716.189296152699.8
5.81-6.710.08616.218599136499.6
6.71-8.220.07117.37324116499.4
8.22-11.630.05820.37571092899.5
11.630.04918.31309953595.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1j09

1j09


Resolution: 2.6→48.175 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7231 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 32.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 2072 5.05 %
Rwork0.2233 --
obs0.2264 41004 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.79 Å2 / Biso mean: 37.4745 Å2 / Biso min: 1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7526 0 23 289 7838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027735
X-RAY DIFFRACTIONf_angle_d0.68210489
X-RAY DIFFRACTIONf_chiral_restr0.0471136
X-RAY DIFFRACTIONf_plane_restr0.0031355
X-RAY DIFFRACTIONf_dihedral_angle_d13.4352803
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.66050.31621130.26282360247389
2.6605-2.7270.32581420.2682396253892
2.727-2.80080.32941370.25362531266895
2.8008-2.88320.31841520.24942509266197
2.8832-2.97620.32671280.25242584271298
2.9762-3.08260.32921260.2342630275698
3.0826-3.2060.32971260.23812589271598
3.206-3.35180.27041370.2352579271697
3.3518-3.52850.3461450.24182580272597
3.5285-3.74950.32611440.2222636278099
3.7495-4.03890.26491380.20672641277999
4.0389-4.44510.22591320.19322681281399
4.4451-5.08770.23761440.19332687283199
5.0877-6.40750.26781510.221327162867100
6.4075-48.18340.23881570.21212813297098
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)
10.02530.00470.04410.01450.02260.0880.00840.00150.0044-0.00640.0582-0.01090.0955-0.1220.0874-0.1002-0.1767-0.0582-0.0204-0.06990.0059-22.346318.9554-20.1414
20.02640.00210.0053-0.00230.00260.0236-0.01420.05220.00650.0162-0.0025-0.0488-0.02170.02140.0153-0.0486-0.0477-0.0650.0501-0.06790.0231-3.402918.22450.534
30.04150.00390.02990.00630.00410.0192-0.0023-0.07470.01010.0301-0.0179-0.01080.00040.017-0.0378-0.0517-0.0659-0.02560.087-0.01420.06453.558220.21045.2432
40.0253-0.0333-0.01770.06670.05530.0540.03540.04050.0001-0.02050.0211-0.02850.0370.0880.02710.01540.0436-0.05860.0713-0.13660.1589-1.52219.6911-11.1056
50.0692-0.0459-0.00230.0472-0.03140.0331-0.00870.04840.0367-0.0539-0.0023-0.05220.0799-0.05170.0073-0.1219-0.03510.01610.0372-0.0356-0.0037-13.465314.649-26.072
60.21440.0080.1340.0635-0.04840.4130.09750.0434-0.06890.03130.03880.01110.1404-0.09880.13970.04790.00420.0330.0403-0.03170.0783-23.515821.3927-41.3868
70.0385-0.0315-0.01690.0618-0.01280.03230.04740.0642-0.0271-0.04840.00330.01270.0301-0.03170.05160.12280.1264-0.04580.25520.03570.3101-35.322241.9384-47.9246
80.0344-0.0163-0.02240.0655-0.01120.02030.02120.02660.0753-0.00730.017-0.0214-0.01-0.02280.04450.17960.0940.0540.24520.16160.185-20.767743.033-53.0735
90.0213-0.01220.02280.013-0.01520.0264-0.00280.01090.0462-0.0316-0.009-0.0209-0.0149-0.0433-0.00430.49740.3210.0770.54280.17640.3577-24.423745.2679-73.1791
100.0003-0.0130.00940.0224-0.03450.02220.04480.02920.0787-0.0951-0.060.072-0.0839-0.0160.00540.41430.2674-0.01140.3670.12340.4997-22.889648.6435-61.3556
110.05450.02630.02530.0235-0.03310.16930.02220.05540.0261-0.0350.04290.03620.0522-00.12410.03680.0340.00830.01260.05250.0563-6.276219.1213-78.6684
120.0131-0.01220.02540.0908-0.0620.1182-0.0258-0.02670.0025-0.0568-0.01730.0642-0.0692-0.03940.00920.19520.0410.01210.1359-0.05140.0795-24.940518.0106-99.6286
130.0347-0.00440.00610.0011-0.00180.00030.0040.0462-0.0086-0.0129-0.00580.03070.019-0.0579-0.02410.2232-0.0811-0.14080.22180.03360.1478-31.990220.0133-104.4065
140.0309-0.01840.03110.1351-0.02710.16830.028-0.04620.0199-0.00310.06680.13590.1512-0.12090.19080.2306-0.0222-0.01970.05930.0520.0515-18.115113.483-76.7333
150.2074-0.0463-0.04460.14550.02670.26150.0959-0.03130.06110.01080.06020.0262-0.00270.00530.29270.00610.04490.06160.0762-0.0023-0.0157-5.326421.511-57.4227
160.0029-0.0019-0.00150.00670.0031-0.0004-0.0092-0.02020.03250.00760.0076-0.03840.00430.0251-0.0396-0.02460.00870.05510.01-0.0580.08230.989439.9647-49.8773
170.00940.01480.0150.02180.0210.02070.022-0.04970.04640.102-0.05550.0807-0.0185-0.0139-0.06940.3287-0.16390.09280.1677-0.04330.1663-7.084246.7056-28.872
180.0157-0.0095-0.00380.0520.00660.00260.0676-0.04970.06960.0704-0.0530.1187-0.0212-0.02650.02230.0471-0.14690.00480.1359-0.10840.152-6.958347.9454-35.2854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3:87)A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 88:123)A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 124:156)A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 157:195)A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 196:294)A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 295:346)A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 347:369)A0
8X-RAY DIFFRACTION8CHAIN A AND (RESID 370:405)A0
9X-RAY DIFFRACTION9CHAIN A AND (RESID 406:455)A0
10X-RAY DIFFRACTION10CHAIN A AND (RESID 456:490)A0
11X-RAY DIFFRACTION11CHAIN B AND (RESID 3:87)B0
12X-RAY DIFFRACTION12CHAIN B AND (RESID 88:123)B0
13X-RAY DIFFRACTION13CHAIN B AND (RESID 124:156)B0
14X-RAY DIFFRACTION14CHAIN B AND (RESID 157:294)B0
15X-RAY DIFFRACTION15CHAIN B AND (RESID 295:346)B0
16X-RAY DIFFRACTION16CHAIN B AND (RESID 347:386)B0
17X-RAY DIFFRACTION17CHAIN B AND (RESID 387:439)B0
18X-RAY DIFFRACTION18CHAIN B AND (RESID 440:490)B0

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