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- PDB-3p8y: Crystal structure of the archaeal asparagine synthetase A complex... -

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Basic information

Entry
Database: PDB / ID: 3p8y
TitleCrystal structure of the archaeal asparagine synthetase A complexed with L-Asparagine
ComponentsAsnS-like asparaginyl-tRNA synthetase related protein
KeywordsLIGASE / asn synthetase bound to Asn / seven stranded anti parallel beta sheet / synthetase / Asp / Asn / AMP / ammonia / LYGASE
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
ASPARAGINE / 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)68,5274
Polymers68,2632
Non-polymers2642
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-56 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.110, 61.280, 156.450
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-ASN / ASPARAGINE / Asparagine


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
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: ID23-2
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 52660 / Num. obs: 51062 / Observed criterion σ(F): 2.63 / Observed criterion σ(I): 2.63
Reflection shellResolution: 1.8→50 Å / % possible all: 97

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.812 Å / SU ML: 0.21 / σ(F): 2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 2000 3.92 %random
Rwork0.1725 ---
obs0.1741 51040 96.94 %-
all-51040 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.933 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0519 Å2-0 Å20 Å2
2---1.3756 Å20 Å2
3---3.4274 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 18 453 5285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064952
X-RAY DIFFRACTIONf_angle_d1.0296680
X-RAY DIFFRACTIONf_dihedral_angle_d13.3551898
X-RAY DIFFRACTIONf_chiral_restr0.075694
X-RAY DIFFRACTIONf_plane_restr0.004864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.30121290.23293317X-RAY DIFFRACTION94
1.845-1.89490.28011430.21013350X-RAY DIFFRACTION94
1.8949-1.95070.26961430.23396X-RAY DIFFRACTION95
1.9507-2.01360.27821420.19613421X-RAY DIFFRACTION96
2.0136-2.08560.22261340.18413451X-RAY DIFFRACTION96
2.0856-2.16910.23291470.17463450X-RAY DIFFRACTION97
2.1691-2.26780.2131340.1713523X-RAY DIFFRACTION98
2.2678-2.38730.23421450.17243513X-RAY DIFFRACTION98
2.3873-2.53690.21381530.1763554X-RAY DIFFRACTION99
2.5369-2.73270.21811430.17833563X-RAY DIFFRACTION99
2.7327-3.00760.21621450.18233572X-RAY DIFFRACTION99
3.0076-3.44260.23531450.16933589X-RAY DIFFRACTION98
3.4426-4.33640.15791470.14393620X-RAY DIFFRACTION98
4.3364-38.82120.16871500.15143721X-RAY DIFFRACTION96
Refinement TLS params.

T12: 0.0018 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.380700.0260.3817-0.14120.6169-0.0198-0.00730.0904-0.0061-0.0106-0.0563-0.0576-0.00560.03130.0697-0.00030.0634-0.00520.1186-19.08966.00147.9257
20.62090.0201-0.02950.4493-0.3580.552-0.0165-0.167-0.09330.0717-0.0211-0.080.12330.00990.03590.14380.00310.1240.02650.0839-15.6379-14.26828.2674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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