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- PDB-2gi3: Crystal structure of Glutamyl-tRNA(Gln) amidotransferase subunit ... -

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Basic information

Entry
Database: PDB / ID: 2gi3
TitleCrystal structure of Glutamyl-tRNA(Gln) amidotransferase subunit A (tm1272) from THERMOTOGA MARITIMA at 1.80 A resolution
ComponentsGlutamyl-tRNA(Gln) amidotransferase subunit A
KeywordsLIGASE / tm1272 / Glutamyl-tRNA(Gln) amidotransferase subunit A (Glu-ADT subunit A) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / translation / ATP binding
Similarity search - Function
Helix Hairpins - #860 / Glutamyl-tRNA(Gln) amidotransferase A subunit / Amidase / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase ...Helix Hairpins - #860 / Glutamyl-tRNA(Gln) amidotransferase A subunit / Amidase / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Helix Hairpins / Helix non-globular / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Glutamyl-tRNA(Gln) amidotransferase subunit A
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Glutamyl-tRNA(Gln) amidotransferase subunit A (tm1272) from THERMOTOGA MARITIMA at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING DATA SUPPORT THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamyl-tRNA(Gln) amidotransferase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7937
Polymers53,2611
Non-polymers5326
Water6,107339
1
A: Glutamyl-tRNA(Gln) amidotransferase subunit A
hetero molecules

A: Glutamyl-tRNA(Gln) amidotransferase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,58514
Polymers106,5222
Non-polymers1,06312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6400 Å2
ΔGint-96 kcal/mol
Surface area33080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.776, 131.776, 61.987
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

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Components

#1: Protein Glutamyl-tRNA(Gln) amidotransferase subunit A / Glu-ADT subunit A


Mass: 53261.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: gatA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0Z9, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 56.2 %
Crystal growTemperature: 277 K / pH: 4.6
Details: 0.02M CaCl2, 30.0% MPD, 0.1M Acetate pH 4.6 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.918381, 0.978662
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2006
Details: 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
RadiationMonochromator: Double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9183811
20.9786621
ReflectionResolution: 1.8→29.91 Å / Num. obs: 57320 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.155 / Rsym value: 0.155 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value% possible all
1.8-1.8598.34.40.729141200.72998.3
1.85-1.999.45.20.6531.140740.653
1.9-1.951006.70.5891.340070.589
1.95-2.011007.30.4861.538870.486
2.01-2.081007.30.4241.737910.424
2.08-2.151007.30.3521.936250.352
2.15-2.231007.40.2792.735350.279
2.23-2.321007.40.2343.233680.234
2.32-2.431007.40.2033.732650.203
2.43-2.551007.30.1854.131090.185
2.55-2.681007.30.1574.829750.157
2.68-2.851007.30.135.827990.13
2.85-3.041007.30.1126.626360.112
3.04-3.291007.20.0888.124890.088
3.29-3.61007.20.0788.622610.078
3.6-4.021007.10.0748.720790.074
4.02-4.651006.80.0649.818360.064
4.65-5.6998.96.60.05611.415420.056
5.69-8.051007.30.0571112290.057
8.05-29.9198.26.90.04812.36930.048

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.91 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.369 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.099
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2907 5.1 %RANDOM
Rwork0.175 ---
all0.176 ---
obs0.17628 57293 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.706 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 36 339 3848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223640
X-RAY DIFFRACTIONr_bond_other_d0.0020.022523
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9884924
X-RAY DIFFRACTIONr_angle_other_deg0.98436163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2125450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62623.595153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34815645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4411528
X-RAY DIFFRACTIONr_chiral_restr0.0890.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
X-RAY DIFFRACTIONr_nbd_refined0.2070.2766
X-RAY DIFFRACTIONr_nbd_other0.1950.22754
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21774
X-RAY DIFFRACTIONr_nbtor_other0.0860.21893
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2309
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0190.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.214
X-RAY DIFFRACTIONr_mcbond_it2.39532475
X-RAY DIFFRACTIONr_mcbond_other0.573916
X-RAY DIFFRACTIONr_mcangle_it2.91953679
X-RAY DIFFRACTIONr_scbond_it5.52581483
X-RAY DIFFRACTIONr_scangle_it7.143111245
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 201 -
Rwork0.275 3914 -
all-4115 -
obs--97.88 %

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