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- PDB-2f2a: Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Gln -

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Basic information

Entry
Database: PDB / ID: 2f2a
TitleStructure of tRNA-Dependent Amidotransferase GatCAB complexed with Gln
Components
  • (Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit ...) x 2
  • Glutamyl-tRNA(Gln) amidotransferase subunit A
KeywordsLIGASE / tRNA / amidotransferase / Structural Genomics
Function / homology
Function and homology information


asparaginyl-tRNA synthase (glutamine-hydrolyzing) activity / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNAGln biosynthesis via transamidation / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / regulation of translational fidelity / translation / ATP binding
Similarity search - Function
Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase superfamily, subunit C / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase C subunit, N-terminal domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E ...Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase superfamily, subunit C / Glu-tRNAGln amidotransferase C subunit / Glu-tRNAGln amidotransferase C subunit, N-terminal domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E / GatB/GatE catalytic domain / Glutamyl-tRNA(Gln) amidotransferase subunit B signature. / Asn/Gln amidotransferase / GatB domain / GatB domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2 / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / Amidase / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Glutamine synthetase/guanido kinase, catalytic domain / Histone, subunit A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / Glutamyl-tRNA(Gln) amidotransferase subunit A / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNakamura, A. / Yao, M. / Tanaka, I.
CitationJournal: Science / Year: 2006
Title: Ammonia channel couples glutaminase with transamidase reactions in GatCAB
Authors: Nakamura, A. / Yao, M. / Chimnaronk, S. / Sakai, N. / Tanaka, I.
History
DepositionNov 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_asym_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_asym_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.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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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
B: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
C: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1035
Polymers118,9333
Non-polymers1702
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-78 kcal/mol
Surface area36790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.187, 88.222, 183.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 52858.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MU50 / Gene: SAV1900 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: P63488, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor

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Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit ... , 2 types, 2 molecules BC

#2: Protein Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Glu/Asp-tRNA(Gln/Asn) amidotransferase B subunit / Asp/Glu-ADT subunit B


Mass: 54794.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MU50 / Gene: SAV1899 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: P64201, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#3: Protein Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C / Glu/Asp-tRNA(Gln/Asn) amidotransferase C subunit / Asp/Glu-ADT subunit C


Mass: 11279.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MU50 / Gene: SAV1901 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: P68807, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor

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Non-polymers , 3 types, 395 molecules

#4: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG MME 550, 0.005M magnesium chloride, 0.05M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 56446 / Num. obs: 56446 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 30.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 4.028 / Num. unique all: 5570 / Rsym value: 0.436 / % possible all: 99.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G5H

2g5h


Resolution: 2.3→20 Å / Data cutoff high absF: 2715052.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 5525 9.8 %RANDOM
Rwork0.211 ---
obs0.211 56332 99.8 %-
all-56332 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.285 Å2 / ksol: 0.318461 e/Å3
Displacement parametersBiso mean: 48.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.32 Å20 Å20 Å2
2--6.2 Å20 Å2
3----11.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7697 0 1 393 8091
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 897 9.7 %
Rwork0.251 8353 -
obs--99.8 %

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