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- PDB-6b1z: Crystal Structure of Glutamate-tRNA Synthetase from Elizabethking... -

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Basic information

Entry
Database: PDB / ID: 6b1z
TitleCrystal Structure of Glutamate-tRNA Synthetase from Elizabethkingia anophelis
ComponentsGlutamate--tRNA ligase
KeywordsLIGASE / SSGCID / Elizabethkingia anophelis / Glutamate--tRNA ligase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 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 / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / Glutamyl/glutaminyl-tRNA synthetase ...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 / 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 / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Glutamate--tRNA ligase / Glutamate--tRNA ligase
Similarity search - Component
Biological speciesElizabethkingia anophelis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Glutamate-tRNA Synthetase from Elizabethkingia anophelis
Authors: Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Oct 4, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,83225
Polymers58,6371
Non-polymers1,19524
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint10 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.170, 99.780, 132.590
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: 58636.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis (bacteria) / Gene: gltX, AYC66_05715 / Plasmid: ElanA.01348.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A1T3FQP0, UniProt: A0A077E909*PLUS, glutamate-tRNA ligase
#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: ElanA.01348.a.B1.PW38250 at 18.25 mg/ml was mixed 1:1 with JCSG+ (a5): 0.2 M magnesium formate, 20% (w/v) PEG-3350, cryoprotected with 20% ethylene glycol. Tray: 292004a5, puck: qrh6-5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→44.441 Å / Num. obs: 83273 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.052 % / Biso Wilson estimate: 20.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.039 / Χ2: 1.04 / Net I/σ(I): 26.47 / Num. measured all: 503995 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.646.120.463.5137374610861070.9090.503100
1.64-1.696.1140.374.4336279593459340.9370.404100
1.69-1.746.150.2955.5835462577057660.9580.32399.9
1.74-1.796.1420.2337.1934354559455930.9710.254100
1.79-1.856.1390.1819.2333527546454610.9820.19899.9
1.85-1.916.1340.13512.3132374528352780.9910.14799.9
1.91-1.986.1140.10116.1931242511951100.9940.1199.8
1.98-2.076.0970.07820.9329821491148910.9960.08699.6
2.07-2.166.0620.06225.7928692474447330.9980.06899.8
2.16-2.266.0530.05230.0627256452045030.9980.05799.6
2.26-2.396.0270.04534.4225797429342800.9990.0599.7
2.39-2.536.0180.03939.4424353407140470.9990.04399.4
2.53-2.75.9780.03543.4122997386838470.9990.03999.5
2.7-2.925.9810.03148.4221352360635700.9990.03499
2.92-3.25.9940.02554.7119745332232940.9990.02899.2
3.2-3.585.9350.02360.4717828301830040.9990.02599.5
3.58-4.135.9570.0265.52159182687267210.02299.4
4.13-5.065.9160.01867.22135532296229110.0299.8
5.06-7.165.8020.01765.92105891826182510.01999.9
7.16-44.4415.1380.0264.035482109110670.9990.02297.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JA2

2ja2


Resolution: 1.6→44.441 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 1941 2.39 %
Rwork0.1778 79158 -
obs0.1786 81099 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.3 Å2 / Biso mean: 32.6223 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 1.6→44.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 0 77 579 4494
Biso mean--54.78 40.51 -
Num. residues----495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064071
X-RAY DIFFRACTIONf_angle_d0.7635495
X-RAY DIFFRACTIONf_chiral_restr0.051594
X-RAY DIFFRACTIONf_plane_restr0.005719
X-RAY DIFFRACTIONf_dihedral_angle_d10.5512455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5999-1.63990.26131250.21095241536691
1.6399-1.68430.24391280.19755328545693
1.6843-1.73380.2281320.19545387551994
1.7338-1.78980.23971370.20055472560996
1.7898-1.85380.2141340.20095577571197
1.8538-1.9280.26021390.18995627576698
1.928-2.01570.20541420.18455700584299
2.0157-2.1220.21461400.18135708584899
2.122-2.2550.20721420.18665751589399
2.255-2.42910.22031410.18285744588599
2.4291-2.67350.2191420.1825775591799
2.6735-3.06020.23321430.1835824596799
3.0602-3.85520.19131440.16765883602799
3.8552-44.45860.1911520.161561416293100
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)
11.8734-1.273-0.74723.7332-0.5472.67050.00230.074-0.1240.12640.00260.2327-0.0597-0.24910.00320.12770.0105-0.00580.1436-0.00710.123844.106234.5488117.9989
20.9953-0.12950.32270.8688-0.48521.4046-0.08620.01460.00450.07110.10130.142-0.0463-0.2469-0.00350.11630.00160.03110.14930.01130.170632.053149.557102.5877
30.1399-0.54140.17862.8667-1.17060.70350.0459-0.0035-0.0058-0.1625-0.03540.03520.10480.00350.00780.1436-0.0126-0.01310.17970.00010.137650.363220.4011115.1423
40.9688-1.36070.40762.1416-0.10861.5865-0.4168-0.5098-0.77150.2584-0.1704-0.57861.00790.55260.00320.63270.14190.15510.42820.24230.620962.5409-17.734125.7549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 65 )A2 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 201 )A66 - 201
3X-RAY DIFFRACTION3chain 'A' and (resid 202 through 424 )A202 - 424
4X-RAY DIFFRACTION4chain 'A' and (resid 425 through 501 )A425 - 501

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