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- PDB-1zq1: Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcu... -

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Basic information

Entry
Database: PDB / ID: 1zq1
TitleStructure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi
Components
  • Glutamyl-tRNA(Gln) amidotransferase subunit D
  • Glutamyl-tRNA(Gln) amidotransferase subunit E
KeywordsLYASE / x-ray / 3D structure / asparaginase 1 family / GatD subfamily
Function / homology
Function and homology information


Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / aminoacyl-tRNA ligase activity / asparaginase activity / amino acid metabolic process / regulation of translational fidelity / translation / ATP binding / cytoplasm
Similarity search - Function
GatB domain, N-terminal subdomain / SH3 type barrels. - #520 / Glutamyl-tRNA(Gln) amidotransferase subunit E / Glutamyl-tRNA(Gln) amidotransferase subunit D / GatD, N-terminal superfamily / GatD, N-terminal / GatD N-terminal domain / GAD-like domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic ...GatB domain, N-terminal subdomain / SH3 type barrels. - #520 / Glutamyl-tRNA(Gln) amidotransferase subunit E / Glutamyl-tRNA(Gln) amidotransferase subunit D / GatD, N-terminal superfamily / GatD, N-terminal / GatD N-terminal domain / GAD-like domain / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 / 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 amidotransferase subunit B-like / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2 / GAD domain / GAD domain / GAD-like domain superfamily / Type I L-asparaginase family / L-asparaginase, N-terminal domain / Rossmann fold - #40 / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Gyrase A; domain 2 / SH3 type barrels. / DNA polymerase; domain 1 / Roll / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / Glutamyl-tRNA(Gln) amidotransferase subunit D / Glutamyl-tRNA(Gln) amidotransferase subunit E
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsSchmitt, E. / Panvert, M. / Blanquet, S. / Mechulam, Y.
CitationJournal: Structure / Year: 2005
Title: Structural Basis for tRNA-Dependent Amidotransferase Function
Authors: Schmitt, E. / Panvert, M. / Blanquet, S. / Mechulam, Y.
History
DepositionMay 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version 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 D
B: Glutamyl-tRNA(Gln) amidotransferase subunit D
C: Glutamyl-tRNA(Gln) amidotransferase subunit E
D: Glutamyl-tRNA(Gln) amidotransferase subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,5266
Polymers243,2604
Non-polymers2662
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17950 Å2
ΔGint-46 kcal/mol
Surface area73390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.700, 138.200, 134.400
Angle α, β, γ (deg.)90.00, 109.60, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein Glutamyl-tRNA(Gln) amidotransferase subunit D / E.C.6.3.5.- / Glu-ADT subunit D


Mass: 49640.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: gatD / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): B834-De3
References: UniProt: Q9V0T9, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#2: Protein Glutamyl-tRNA(Gln) amidotransferase subunit E / E.C.6.3.5.- / Glu-ADT subunit E


Mass: 71989.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: gatE / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): B834-De3
References: UniProt: Q9V0U0, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor
#3: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.7 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 20000, Dioxane, Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97576,0.97956
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2005
RadiationMonochromator: DIAMOND / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.975761
20.979561
ReflectionResolution: 3→50 Å / Num. all: 137974 / Num. obs: 137974 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 82.6 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069
Reflection shellResolution: 3→3.1 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.374 / Num. unique all: 13148 / Rsym value: 0.374 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 3→50 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 4278 -random
Rwork0.217 ---
all0.2171 70835 --
obs0.2171 70028 98.9 %-
Displacement parametersBiso mean: 67.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.503 Å20 Å2-4.151 Å2
2---11.682 Å20 Å2
3---10.179 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14783 0 18 68 14869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.454
X-RAY DIFFRACTIONc_bond_d0.0075
LS refinement shellResolution: 3→3.02 Å
RfactorNum. reflection
Rfree0.372 94
Rwork0.383 -
obs-1400

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