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- PDB-3h0m: Structure of trna-dependent amidotransferase gatcab from aquifex ... -

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Basic information

Entry
Database: PDB / ID: 3h0m
TitleStructure of trna-dependent amidotransferase gatcab from aquifex aeolicus
Components
  • (Glutamyl-tRNA(Gln) amidotransferase subunit ...) x 2
  • Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
KeywordsLIGASE / MULTI PROTEIN COMPLEX / Protein biosynthesis
Function / homologyGlutamine synthetase/guanido kinase, catalytic domain / Glu-tRNAGln amidotransferase superfamily, subunit C / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, C-terminal / Amidase, conserved site / Asn/Gln amidotransferase / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit ...Glutamine synthetase/guanido kinase, catalytic domain / Glu-tRNAGln amidotransferase superfamily, subunit C / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, C-terminal / Amidase, conserved site / Asn/Gln amidotransferase / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, subunit B /E / Glutamyl-tRNA(Gln) amidotransferase, subunit B, conserved site / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit / Glutamyl-tRNA(Gln) amidotransferase A subunit / Glu-tRNAGln amidotransferase C subunit / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / Amidase / Amidase signature (AS) superfamily / Amidase / GatB domain / Glu-tRNAGln amidotransferase C subunit / GatB/GatE catalytic domain / Amidases signature. / Glutamyl-tRNA(Gln) amidotransferase subunit B signature. / Amidase signature domain / glutaminyl-tRNAGln biosynthesis via transamidation / glutamyl-tRNA(Gln) amidotransferase complex / glutaminyl-tRNA synthase (glutamine-hydrolysing) / Ligases, Forming carbon-nitrogen bonds, Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / mitochondrial translation / amidase activity / regulation of translational fidelity / translation / mitochondrion / ATP binding / Glutamyl-tRNA(Gln) amidotransferase subunit A / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B / Glutamyl-tRNA(Gln) amidotransferase subunit C
Function and homology information
Specimen sourceAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.8 Å resolution
AuthorsWu, J. / Bu, W. / Sheppard, K. / Kitabatake, M. / Soll, D. / Smith, J.L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Insights into tRNA-Dependent Amidotransferase Evolution and Catalysis from the Structure of the Aquifex aeolicus Enzyme
Authors: Wu, J. / Bu, W. / Sheppard, K. / Kitabatake, M. / Kwon, S.T. / Soll, D. / Smith, J.L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 9, 2009 / Release: Jul 21, 2009
RevisionDateData content typeGroupProviderType
1.0Jul 21, 2009Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamyl-tRNA(Gln) amidotransferase subunit A
B: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
C: Glutamyl-tRNA(Gln) amidotransferase subunit C
D: Glutamyl-tRNA(Gln) amidotransferase subunit A
E: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
F: Glutamyl-tRNA(Gln) amidotransferase subunit C
G: Glutamyl-tRNA(Gln) amidotransferase subunit A
H: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
I: Glutamyl-tRNA(Gln) amidotransferase subunit C
J: Glutamyl-tRNA(Gln) amidotransferase subunit A
K: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
L: Glutamyl-tRNA(Gln) amidotransferase subunit C
M: Glutamyl-tRNA(Gln) amidotransferase subunit A
N: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
O: Glutamyl-tRNA(Gln) amidotransferase subunit C
P: Glutamyl-tRNA(Gln) amidotransferase subunit A
Q: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
R: Glutamyl-tRNA(Gln) amidotransferase subunit C
S: Glutamyl-tRNA(Gln) amidotransferase subunit A
T: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
U: Glutamyl-tRNA(Gln) amidotransferase subunit C
V: Glutamyl-tRNA(Gln) amidotransferase subunit A
W: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
X: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)961,43447
Polyers959,57124
Non-polymers1,86323
Water0
1
A: Glutamyl-tRNA(Gln) amidotransferase subunit A
B: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
C: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1826
Polyers119,9463
Non-polymers2363
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11190
ΔGint (kcal/M)-81
Surface area (Å2)39550
MethodPISA
2
D: Glutamyl-tRNA(Gln) amidotransferase subunit A
E: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
F: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1585
Polyers119,9463
Non-polymers2122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11040
ΔGint (kcal/M)-67
Surface area (Å2)39580
MethodPISA
3
G: Glutamyl-tRNA(Gln) amidotransferase subunit A
H: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
I: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1826
Polyers119,9463
Non-polymers2363
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11260
ΔGint (kcal/M)-77
Surface area (Å2)39300
MethodPISA
4
J: Glutamyl-tRNA(Gln) amidotransferase subunit A
K: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
L: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1826
Polyers119,9463
Non-polymers2363
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11180
ΔGint (kcal/M)-79
Surface area (Å2)39420
MethodPISA
5
M: Glutamyl-tRNA(Gln) amidotransferase subunit A
N: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
O: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1826
Polyers119,9463
Non-polymers2363
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11180
ΔGint (kcal/M)-76
Surface area (Å2)39480
MethodPISA
6
P: Glutamyl-tRNA(Gln) amidotransferase subunit A
Q: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
R: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1826
Polyers119,9463
Non-polymers2363
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11200
ΔGint (kcal/M)-77
Surface area (Å2)39440
MethodPISA
7
S: Glutamyl-tRNA(Gln) amidotransferase subunit A
T: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
U: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1826
Polyers119,9463
Non-polymers2363
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11210
ΔGint (kcal/M)-82
Surface area (Å2)39560
MethodPISA
8
V: Glutamyl-tRNA(Gln) amidotransferase subunit A
W: Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
X: Glutamyl-tRNA(Gln) amidotransferase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1826
Polyers119,9463
Non-polymers2363
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11180
ΔGint (kcal/M)-80
Surface area (Å2)39660
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)128.248, 129.856, 155.069
Angle α, β, γ (deg.)90.01, 89.96, 90.11
Int Tables number1
Space group name H-MP 1

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Components

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Glutamyl-tRNA(Gln) amidotransferase subunit ... , 2 types, 16 molecules ADGJMPSVCFILORUX

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


Mass: 53589.160 Da / Num. of mol.: 8 / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_247, gatA, GATCA / Plasmid name: pET17b-CA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O66610, Ligases, Forming carbon-nitrogen bonds, Carbon-nitrogen ligases with glutamine as amido-N-donor
#3: Protein/peptide
Glutamyl-tRNA(Gln) amidotransferase subunit C / Glu-ADT subunit C


Mass: 11228.740 Da / Num. of mol.: 8 / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: gatC, aq_2149 / Plasmid name: pET17b-CA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O67904, Ligases, Forming carbon-nitrogen bonds, Carbon-nitrogen ligases with glutamine as amido-N-donor

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Protein/peptide , 1 types, 8 molecules BEHKNQTW

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


Mass: 55128.535 Da / Num. of mol.: 8 / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_461, gatB / Plasmid name: pET17b-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O66766, Ligases, Forming carbon-nitrogen bonds, Carbon-nitrogen ligases with glutamine as amido-N-donor

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Non-polymers , 3 types, 23 molecules

#4: Chemical
ChemComp-GLN / GLUTAMINE


Mass: 146.144 Da / Num. of mol.: 8 / Formula: C5H10N2O3 / Glutamine
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Formula: Mg / Magnesium
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn / Zinc

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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: 2.69 / Density percent sol: 54.3 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1:1 ratio of Protein solution (6-9mg/ml GatCAB,10mM HEPES, 50uM Zn acetate,10mM Gln, 0.6mM ATP) mix with well solution (10-12% PEG3350, 10mM Mg formate), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0274 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Collection date: Dec 19, 2005
RadiationMonochromator: MIRRORS / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0274 Å / Relative weight: 1
ReflectionD resolution high: 2.8 Å / D resolution low: 39.4 Å / Number all: 241473 / Number obs: 241473 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.061 / Rsym value: 0.061 / NetI over sigmaI: 11.5 / Redundancy: 2 % / Percent possible obs: 98
Reflection shellRmerge I obs: 0.478 / Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / MeanI over sigI obs: 1.6 / Rsym value: 0.478 / Redundancy: 1.9 % / Percent possible all: 96.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2H0L
Correlation coeff Fo to Fc: 0.928 / Correlation coeff Fo to Fc free: 0.894 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 20.982 / Overall SU ML: 0.412 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.91 / Overall ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.4 Å / Solvent model details: BABINET MODEL WITH MASK
Displacement parametersB iso mean: 61.581 Å2 / Aniso B11: -4.1 Å2 / Aniso B12: 0.42 Å2 / Aniso B13: 0.33 Å2 / Aniso B22: 8.81 Å2 / Aniso B23: 1.49 Å2 / Aniso B33: -4.7 Å2
Least-squares processR factor R free: 0.3054 / R factor R work: 0.25364 / R factor obs: 0.25623 / Highest resolution: 2.8 Å / Lowest resolution: 39.37 Å / Number reflection R free: 12256 / Number reflection all: 241468 / Number reflection obs: 229209 / Percent reflection R free: 5.1 / Percent reflection obs: 98
Refine analyzeLuzzati coordinate error free: 0.302 Å / Luzzati coordinate error obs: 0.455 Å
Refine hist #LASTHighest resolution: 2.8 Å / Lowest resolution: 39.37 Å
Number of atoms included #LASTProtein: 62848 / Nucleic acid: 0 / Ligand: 87 / Solvent: 0 / Total: 62935
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02264355
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.98586850
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0105.0007806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85224.4962936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.05715.00011968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.31615.000400
X-RAY DIFFRACTIONr_chiral_restr0.1040.2009488
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02048168
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.20029888
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.20042896
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2001945
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.200138
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.20029
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints ncs

Refine ID: X-RAY DIFFRACTION

Dom IDAuth asym IDEns IDNumberTypeRms dev positionWeight position
1A11912tight positional0.030.05
2D11912tight positional0.040.05
3G11912tight positional0.030.05
4J11912tight positional0.040.05
5M11912tight positional0.030.05
6P11912tight positional0.040.05
7S11912tight positional0.040.05
8V11912tight positional0.030.05
1B22356medium positional0.310.50
2E22356medium positional0.310.50
3H22356medium positional0.300.50
4K22356medium positional0.320.50
5N22356medium positional0.290.50
6Q22356medium positional0.280.50
7T22356medium positional0.270.50
8W22356medium positional0.380.50
1B3957medium positional0.360.50
2E3957medium positional0.360.50
3H3957medium positional0.330.50
4K3957medium positional0.330.50
5N3957medium positional0.340.50
6Q3957medium positional0.320.50
7T3957medium positional0.310.50
8W3957medium positional0.320.50
1C4760medium positional0.320.50
2F4760medium positional0.330.50
3I4760medium positional0.300.50
4L4760medium positional0.330.50
5O4760medium positional0.310.50
6R4760medium positional0.360.50
7U4760medium positional0.300.50
8X4760medium positional0.330.50
1A11876loose positional0.335.00
2D11876loose positional0.395.00
3G11876loose positional0.305.00
4J11876loose positional0.345.00
5M11876loose positional0.335.00
6P11876loose positional0.345.00
7S11876loose positional0.335.00
8V11876loose positional0.325.00
Refine LS shellHighest resolution: 2.8 Å / R factor R free: 0.4 / R factor R work: 0.352 / Lowest resolution: 2.951 Å / Number reflection R free: 1778 / Number reflection R work: 32647 / Total number of bins used: 10 / Percent reflection obs: 95.84

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