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- PDB-3p8t: Crystal structure of the archaeal asparagine synthetase A -

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Basic information

Entry
Database: PDB / ID: 3p8t
TitleCrystal structure of the archaeal asparagine synthetase A
ComponentsAsnS-like asparaginyl-tRNA synthetase related protein
KeywordsLIGASE / anti parallel beta sheet / Asn synthetase / synthetase / AMP / ADP
Function / homology
Function and homology information


aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / ATP binding
Similarity search - Function
Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AsnS-like asparaginyl-tRNA synthetase related protein
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBlaise, M. / Kern, D.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of the Archaeal Asparagine Synthetase: Interrelation with Aspartyl-tRNA and Asparaginyl-tRNA Synthetases.
Authors: Blaise, M. / Frechin, M. / Olieric, V. / Charron, C. / Sauter, C. / Lorber, B. / Roy, H. / Kern, D.
History
DepositionOct 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: AsnS-like asparaginyl-tRNA synthetase related protein
B: AsnS-like asparaginyl-tRNA synthetase related protein


Theoretical massNumber of molelcules
Total (without water)68,2632
Polymers68,2632
Non-polymers00
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-55 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.930, 61.380, 156.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AsnS-like asparaginyl-tRNA synthetase related protein / Archaeal asparagine synthetase


Mass: 34131.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: asnS-like, PYRAB02460, PAB2356 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V228
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM Tris-HCl pH7, 0.2M NaCl and 32% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978 Å
DetectorType: MAR CCD 345 / Detector: CCD / Date: Jun 3, 2006
RadiationMonochromator: SAGITALLY Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 54061 / Num. obs: 54061 / % possible obs: 99.6 % / Observed criterion σ(F): 5.89 / Observed criterion σ(I): 5.89
Reflection shellResolution: 1.78→50 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→48.249 Å / SU ML: 0.16 / σ(F): 1.99 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 1986 3.67 %random
Rwork0.1503 ---
all0.1518 54061 --
obs0.1518 54058 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.767 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0343 Å2-0 Å20 Å2
2---0.8819 Å20 Å2
3---3.9162 Å2
Refinement stepCycle: LAST / Resolution: 1.78→48.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 0 673 5487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064936
X-RAY DIFFRACTIONf_angle_d1.056660
X-RAY DIFFRACTIONf_dihedral_angle_d13.2891892
X-RAY DIFFRACTIONf_chiral_restr0.073692
X-RAY DIFFRACTIONf_plane_restr0.005860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.82450.2231350.1673666X-RAY DIFFRACTION99
1.8245-1.87380.21981500.17043697X-RAY DIFFRACTION100
1.8738-1.9290.23021390.16763630X-RAY DIFFRACTION99
1.929-1.99130.22621300.15643657X-RAY DIFFRACTION100
1.9913-2.06240.21971410.14143696X-RAY DIFFRACTION100
2.0624-2.1450.18011500.14483674X-RAY DIFFRACTION100
2.145-2.24260.23441370.15193667X-RAY DIFFRACTION99
2.2426-2.36090.20721440.15693654X-RAY DIFFRACTION99
2.3609-2.50880.18991450.14823726X-RAY DIFFRACTION100
2.5088-2.70250.21441370.1493716X-RAY DIFFRACTION100
2.7025-2.97440.18821390.15313745X-RAY DIFFRACTION100
2.9744-3.40470.19481450.15343783X-RAY DIFFRACTION100
3.4047-4.28910.1561440.13273783X-RAY DIFFRACTION100
4.2891-48.26660.16331500.15283978X-RAY DIFFRACTION100
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)
10.3788-0.0020.01060.22020.07990.2645-0.0049-0.025-0.0332-0.0022-0.0160.01540.03430.0010.01990.034-0.00060.00060.0276-0.00120.051718.856-6.0647.8864
20.46230.09020.06830.2640.17110.3956-0.0163-0.14840.08960.0341-0.040.0643-0.0664-0.02930.05420.0714-0.0036-0.00950.075-0.03590.056115.654414.191828.151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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