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- PDB-3p8v: Crystal structure of the archaeal asparagine synthetase A complex... -

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Basic information

Entry
Database: PDB / ID: 3p8v
TitleCrystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid
ComponentsAsnS-like asparaginyl-tRNA synthetase related protein
KeywordsLIGASE / anti-parallel beta sheet / asparagine synthetase / ATP binding / synthetase / Asp / Asn / AMP / ammonium
Function / homology
Function and homology information


asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / ATP binding / metal ion 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
ASPARTIC ACID / AsnS-like asparaginyl-tRNA synthetase related protein
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AsnS-like asparaginyl-tRNA synthetase related protein
B: AsnS-like asparaginyl-tRNA synthetase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5294
Polymers68,2632
Non-polymers2662
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-56 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.330, 61.500, 155.990
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: Chemical ChemComp-ASP / ASPARTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM Tris-HCl pH7, 0.2M NaCl and 32% PEG3350 and soak in 1 to 5mM aspartic acid, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 1, 2006
RadiationMonochromator: horizontally diffracting Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 52908 / Num. obs: 51846 / Observed criterion σ(F): 2.38 / Observed criterion σ(I): 2.38
Reflection shellResolution: 1.8→50 Å / % possible all: 98

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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: 1.8→48.293 Å / SU ML: 0.2 / σ(F): 1.99 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 2014 3.89 %random
Rwork0.1759 ---
all0.1775 51829 --
obs0.1775 51829 97.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.631 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3162 Å2-0 Å20 Å2
2---1.1656 Å20 Å2
3---1.4818 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 18 500 5332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054952
X-RAY DIFFRACTIONf_angle_d0.8826680
X-RAY DIFFRACTIONf_dihedral_angle_d12.3121898
X-RAY DIFFRACTIONf_chiral_restr0.066694
X-RAY DIFFRACTIONf_plane_restr0.004864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.24611340.2133220X-RAY DIFFRACTION90
1.845-1.89490.23171430.19343364X-RAY DIFFRACTION94
1.8949-1.95070.23411320.18343520X-RAY DIFFRACTION98
1.9507-2.01360.23831560.18093539X-RAY DIFFRACTION99
2.0136-2.08560.2271370.17653595X-RAY DIFFRACTION100
2.0856-2.16910.24121460.17933580X-RAY DIFFRACTION100
2.1691-2.26780.25381400.17463581X-RAY DIFFRACTION100
2.2678-2.38740.21111390.17973581X-RAY DIFFRACTION100
2.3874-2.5370.2531520.17793610X-RAY DIFFRACTION99
2.537-2.73280.23391400.18053602X-RAY DIFFRACTION99
2.7328-3.00780.23141500.1933600X-RAY DIFFRACTION99
3.0078-3.44290.23051390.18733630X-RAY DIFFRACTION99
3.4429-4.33730.19081510.14993630X-RAY DIFFRACTION98
4.3373-48.31020.17631550.16733763X-RAY DIFFRACTION97
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)
10.5082-0.00760.08970.5963-0.2080.6207-0.00450.0266-0.0633-0.0244-0.026-0.0460.04610.01440.02910.04530.00330.00120.05170.00340.0903-19.0805-6.0515-7.9445
20.4424-0.18010.07180.8856-0.43861.10.02940.18060.1153-0.2006-0.0688-0.1645-0.19470.11950.04010.1816-0.00310.01090.1360.04230.1064-15.68314.2154-28.3174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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