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

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Basic information

Entry
Database: PDB / ID: 3rex
TitleCrystal structure of the archaeal asparagine synthetase A complexed with Adenosine monophosphate
ComponentsAsnS-like asparaginyl-tRNA synthetase related protein
KeywordsLIGASE / Asn synthetase / AMP binding / anti parallel beat sheet
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
ADENOSINE MONOPHOSPHATE / 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. / Frechin, M. / Charron, C. / Roy, H. / Sauter, C. / Lorber, B. / Olieric, V. / 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
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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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)68,9815
Polymers68,2632
Non-polymers7193
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-66 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.380, 60.930, 155.800
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 A


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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 39.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM Tris pH7 0.2M NaCl 32%PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: 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: 51859 / Num. obs: 51859 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 10.54
Reflection shellResolution: 1.8→1.9 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NNH

1nnh


Resolution: 1.8→32.818 Å / SU ML: 0.2 / σ(F): 2.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 1991 3.84 %random
Rwork0.1599 ---
all0.1613 51857 --
obs0.1613 51857 98.98 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.492 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6028 Å2-0 Å20 Å2
2---2.3838 Å20 Å2
3---1.7811 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 47 389 5228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074975
X-RAY DIFFRACTIONf_angle_d1.1016721
X-RAY DIFFRACTIONf_dihedral_angle_d14.4261909
X-RAY DIFFRACTIONf_chiral_restr0.078699
X-RAY DIFFRACTIONf_plane_restr0.005859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.26511410.22233537X-RAY DIFFRACTION100
1.845-1.89490.24321470.2013519X-RAY DIFFRACTION100
1.8949-1.95070.23561380.18883562X-RAY DIFFRACTION100
1.9507-2.01360.21441510.17353550X-RAY DIFFRACTION100
2.0136-2.08560.21871310.16763556X-RAY DIFFRACTION100
2.0856-2.1690.20361490.16583548X-RAY DIFFRACTION100
2.169-2.26770.18441460.15453527X-RAY DIFFRACTION99
2.2677-2.38730.22071380.16253533X-RAY DIFFRACTION99
2.3873-2.53680.21731450.17063582X-RAY DIFFRACTION99
2.5368-2.73260.20691370.16783544X-RAY DIFFRACTION99
2.7326-3.00740.21251410.17063556X-RAY DIFFRACTION99
3.0074-3.44220.20631430.16233578X-RAY DIFFRACTION98
3.4422-4.33520.17891400.13613595X-RAY DIFFRACTION98
4.3352-32.8230.14591440.14143679X-RAY DIFFRACTION96
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)
10.9710.04290.02711.2242-0.25790.9506-0.00430.0301-0.1268-0.0322-0.0324-0.03310.06090.01910.01170.01810.0116-0.0030.0324-0.00790.1201-19.1555-5.9697-7.8423
21.0287-0.17030.15941.0992-0.48881.4352-0.00610.2740.1468-0.256-0.0839-0.1321-0.25180.1740.01060.2384-0.0147-0.00580.17060.05020.1149-15.828814.2045-28.4117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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