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- PDB-2cfo: Non-Discriminating Glutamyl-tRNA Synthetase from Thermosynechococ... -

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Basic information

Entry
Database: PDB / ID: 2cfo
TitleNon-Discriminating Glutamyl-tRNA Synthetase from Thermosynechococcus elongatus in Complex with Glu
ComponentsGLUTAMYL-TRNA SYNTHETASE
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytoplasm
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 / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Glutamyl-tRNA synthetase / Anticodon binding domain / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA Synthetase; domain 2 ...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 / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Glutamyl-tRNA synthetase / Anticodon binding domain / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / 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 / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / 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 speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSchulze, J.O. / Nickel, D. / Schubert, W.-D. / Jahn, D. / Heinz, D.W.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of a Non-Discriminating Glutamyl- tRNA Synthetase.
Authors: Schulze, J.O. / Masoumi, A. / Nickel, D. / Jahn, M. / Jahn, D. / Schubert, W.-D. / Heinz, D.W.
History
DepositionFeb 22, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMYL-TRNA SYNTHETASE
B: GLUTAMYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8703
Polymers110,7232
Non-polymers1471
Water5,621312
1
A: GLUTAMYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5092
Polymers55,3621
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLUTAMYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)55,3621
Polymers55,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.149, 99.603, 182.407
Angle α, β, γ (deg.)90.00, 91.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9889, -0.1479, 0.01484), (-0.1476, -0.9888, -0.02103), (0.01779, 0.01861, -0.9997)
Vector: 18.17, 6.482, 91.46)

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Components

#1: Protein GLUTAMYL-TRNA SYNTHETASE / GLUTAMATE--TRNA LIGASE / GLURS


Mass: 55361.547 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: BP-1 / Plasmid: PET29 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8DLI5, glutamate-tRNA ligase
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.97 Å3/Da / Density % sol: 59 %
Crystal growpH: 5.8
Details: 740 MM NA CITRATE, 140 MM CITRIC ACID, 10 MM DTT, pH 5.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.89974
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 20, 2005 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89974 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 46164 / % possible obs: 96.9 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.2
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.4 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GLN

1gln


Resolution: 2.45→45.6 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.902 / SU B: 18.54 / SU ML: 0.217 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2309 5 %RANDOM
Rwork0.186 ---
obs0.189 43854 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20.3 Å2
2--4.04 Å20 Å2
3----3.3 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7691 0 10 312 8013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227921
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.541.95610773
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4325977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51823.461393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.402151294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7021573
X-RAY DIFFRACTIONr_chiral_restr0.0920.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026173
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1770.23790
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2850.25388
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2400
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.16125027
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.21437757
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.20723388
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.21833012
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 159
Rwork0.245 3014
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)
13.75720.3952-1.51665.1291-1.344210.59480.44710.1755-0.02110.6891-0.3875-0.3708-0.59070.3424-0.0596-0.0321-0.0088-0.0612-0.04710.0502-0.11094.917-14.74240.09
21.1330.0325-0.38680.93570.04951.6030.15170.24670.076-0.1059-0.1448-0.1204-0.0086-0.0154-0.0069-0.289-0.0052-0.04270.0044-0.0068-0.18270.9413.19723.04
31.2406-0.1041-0.10221.6313-1.53382.50260.0484-0.0919-0.1080.15070.06790.01860.0993-0.1973-0.1162-0.2109-0.0073-0.03370.0329-0.06-0.1212-4.369-7.70929.468
41.50410.27921.38990.8728-0.31838.86520.1726-0.2345-0.2446-0.1079-0.10770.13580.3759-0.5347-0.0648-0.0337-0.0531-0.00770.04760.1055-0.0328-0.343-23.22661.187
56.31061.1147-3.18443.889-2.74629.68090.22870.11630.0389-0.09920.09150.1242-0.36390.0053-0.3202-0.1511-0.11510.02430.21670.0879-0.1502-4.324-28.13894.505
66.97653.2729-4.53051.55-2.612619.25810.4715-0.63460.6939-0.0386-0.1513-0.1755-0.61530.2177-0.3202-0.1077-0.06810.02990.0520.1536-0.03682.236-24.7492.205
72.5005-0.5589-0.32692.8184-0.68426.5380.1829-0.23110.0207-0.19410.0722-0.2203-0.10120.187-0.2551-0.24-0.0420.0350.01240.0222-0.1297-9.57122.57551.74
84.98862.8016-0.72743.5750.92472.11120.0129-0.2315-0.08870.2034-0.10340.05370.51310.05460.0905-0.18650.0667-0.00720.02020.0492-0.1876-19.431-1.11771.169
92.4102-0.0039-0.77171.9133-0.26052.06440.0906-0.00190.0921-0.1226-0.0545-0.0777-0.088-0.1233-0.0361-0.2340.02170.0133-0.1132-0.0682-0.1841-21.24615.42466.356
1014.3004-1.426-5.90837.37679.664229.5652-0.39461.5445-1.2981-0.1782-0.58170.37961.1753-2.13110.9763-0.0728-0.1192-0.00070.3193-0.01210.1216-26.50617.42943.274
110.52640.3907-0.53550.559-1.63166.20610.03630.08810.1760.21480.11260.1537-0.5881-0.436-0.149-0.02240.0970.03050.08820.1230.0175-14.33233.61622.162
127.1092-1.33413.51042.5812-2.70279.59020.06180.4788-0.4341-0.1966-0.04550.14210.5438-0.3973-0.0163-0.2291-0.0272-0.01080.10030.1505-0.0746-15.97234.09-1.775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 61
2X-RAY DIFFRACTION2A62 - 155
3X-RAY DIFFRACTION3A156 - 252
4X-RAY DIFFRACTION4A253 - 382
5X-RAY DIFFRACTION5A383 - 454
6X-RAY DIFFRACTION6A455 - 485
7X-RAY DIFFRACTION7B2 - 75
8X-RAY DIFFRACTION8B76 - 148
9X-RAY DIFFRACTION9B149 - 236
10X-RAY DIFFRACTION10B237 - 253
11X-RAY DIFFRACTION11B254 - 428
12X-RAY DIFFRACTION12B429 - 488

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