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- PDB-6b1p: Crystal Structure of Glutamate-tRNA Synthetase from Helicobacter ... -

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Basic information

Entry
Database: PDB / ID: 6b1p
TitleCrystal Structure of Glutamate-tRNA Synthetase from Helicobacter pylori
ComponentsGlutamate--tRNA ligase 1
KeywordsLIGASE / SSGCID / Glutamate--tRNA ligase / Helicobacter pylori / 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 / 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 / : / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 ...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 / : / 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
Glutamate--tRNA ligase 1
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Glutamate-tRNA Synthetase from Helicobacter pylori
Authors: Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate--tRNA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4822
Polymers54,4201
Non-polymers621
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint3 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.050, 44.600, 54.120
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 1 / Glutamyl-tRNA synthetase 1 / GluRS 1


Mass: 54420.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: gltX1, HPG27_434 / Plasmid: HepyC.01187.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5Z6J9, glutamate-tRNA ligase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: HepyC.01187.a.B1.PW38242 at 20.6 mg/ml was mixed 1:1 with JCSG+ (a3): 0.2 M ammonium citrate dibasic, 20% (w/v) PEG-3350, cryoprotected with 15% ethylene glycol. Tray: 291377a3, puck: ben7-8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→43.562 Å / Num. obs: 17766 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.836 % / Biso Wilson estimate: 50.48 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.076 / Χ2: 0.956 / Net I/σ(I): 15.19 / Num. measured all: 103691 / Scaling rejects: 7
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
2.5-2.566.1460.5263.187762126312630.8420.575100
2.56-2.646.110.433.917698126012600.8970.471100
2.64-2.716.1310.34257559123312330.9350.374100
2.71-2.86.0630.2985.717258119811970.9490.32699.9
2.8-2.896.0690.246.926803112111210.9680.262100
2.89-2.995.9940.198.966851114311430.9770.208100
2.99-3.15.9920.14611.076334105710570.9860.16100
3.1-3.235.9220.11812.696242105510540.9920.12999.9
3.23-3.375.8810.09216.095969101510150.9940.101100
3.37-3.545.7950.07518.7454949509480.9950.08399.8
3.54-3.735.670.06121.5552909349330.9970.06799.9
3.73-3.955.6390.05423.7848338588570.9970.05999.9
3.95-4.235.6270.0525.2346258238220.9980.05599.9
4.23-4.565.5310.04527.3843317837830.9970.05100
4.56-55.5870.04528.5840347227220.9970.05100
5-5.595.5740.04227.8935846436430.9980.046100
5.59-6.465.6140.04428.4132565825800.9980.04999.7
6.46-7.915.380.04528.7627065045030.9970.0599.8
7.91-11.185.1160.04930.2520674064040.9940.05499.5
11.18-43.5624.3640.05827.519952432280.9960.06693.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2ja2


Resolution: 2.5→43.562 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.12
RfactorNum. reflection% reflection
Rfree0.2809 1740 10.09 %
Rwork0.2339 --
obs0.2386 17249 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 167.47 Å2 / Biso mean: 63.2034 Å2 / Biso min: 24.68 Å2
Refinement stepCycle: final / Resolution: 2.5→43.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 4 27 3246
Biso mean--66.35 50.73 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033287
X-RAY DIFFRACTIONf_angle_d0.5024468
X-RAY DIFFRACTIONf_chiral_restr0.04513
X-RAY DIFFRACTIONf_plane_restr0.003579
X-RAY DIFFRACTIONf_dihedral_angle_d8.4081956
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.57360.38071350.31321172130791
2.5736-2.65670.30961370.28021210134793
2.6567-2.75160.32751410.27831235137695
2.7516-2.86180.33971410.28281253139495
2.8618-2.9920.35881410.28211282142397
2.992-3.14970.32741430.28831269141298
3.1497-3.34690.29771460.27971297144398
3.3469-3.60520.31641470.24891315146299
3.6052-3.96780.29631460.21811323146999
3.9678-4.54150.23441510.19441347149899
4.5415-5.71970.2651510.213651516100
5.7197-43.56810.22421610.21731441160299
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)
13.76621.59562.81315.9489-1.34553.7623-0.27960.5528-0.2959-0.2392-0.22890.1534-0.38650.30960.36290.4160.03210.01610.3698-0.01480.277269.421237.677329.1129
23.7213-0.40952.89330.8622-0.29582.4625-0.00670.85960.6543-0.0165-0.1751-0.3971-0.27850.65120.24350.6181-0.06770.01070.42940.00890.42164.573148.218728.5481
36.2197-0.68150.19796.30062.3276.91460.0074-0.0533-0.24150.1335-0.29870.68710.1975-1.22350.11730.447-0.00720.06620.3328-0.03350.343937.509244.118930.5469
44.307-0.8584-0.50965.0191-0.2962.0864-0.1959-0.1762-0.41040.13490.39240.1470.13460.1536-0.17980.49590.0575-0.02670.31040.02060.263253.258435.352326.8704
52.0694-0.70810.65152.12080.13543.08480.0827-0.1758-0.24930.13990.1533-0.09460.6029-0.3028-0.28950.4626-0.0003-0.0450.2554-0.02860.506262.907930.077336.6318
63.6853-0.83080.39572.7141-0.0884.35990.31640.239-0.798-0.1785-0.0877-0.22070.88750.741-0.22510.55950.1933-0.07350.4242-0.04930.517778.968325.512937.135
73.2592-0.79333.86523.3015-2.50717.7294-0.21690.36160.06750.00440.06130.179-0.02170.64880.13620.41090.1305-0.03710.64750.04150.428897.398233.94555.1014
83.438-0.0925-2.37223.78180.96281.9428-0.25771.11980.45520.498-0.5602-0.7084-0.13221.08960.31040.4562-0.0254-0.33471.03650.23690.6469111.120129.334566.8363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 48 )A2 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 92 )A49 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 149 )A93 - 149
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 217 )A150 - 217
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 247 )A218 - 247
6X-RAY DIFFRACTION6chain 'A' and (resid 248 through 313 )A248 - 313
7X-RAY DIFFRACTION7chain 'A' and (resid 314 through 380 )A314 - 380
8X-RAY DIFFRACTION8chain 'A' and (resid 381 through 462 )A381 - 462

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