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- PDB-2xgt: Asparaginyl-tRNA synthetase from Brugia malayi complexed with the... -

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Basic information

Entry
Database: PDB / ID: 2xgt
TitleAsparaginyl-tRNA synthetase from Brugia malayi complexed with the sulphamoyl analogue of asparaginyl-adenylate
ComponentsASPARAGINYL-TRNA SYNTHETASE, CYTOPLASMIC
KeywordsLIGASE / ATP-BINDING / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE / :
Similarity search - Component
Biological speciesBRUGIA MALAYI (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCrepin, T. / Haertlein, M. / Kron, M. / Cusack, S.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: A Hybrid Structural Model of the Complete Brugia Malayi Cytoplasmic Asparaginyl-tRNA Synthetase.
Authors: Crepin, T. / Peterson, F. / Haertlein, M. / Jensen, D. / Wang, C. / Cusack, S. / Kron, M.
#1: Journal: J. Comput. Aided Mol. Des. / Year: 2006
Title: Discovering New Classes of Brugia Malayi Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change.
Authors: Sukuru, S.C.K. / Crepin, T. / Milev, Y. / Marsh, L.C. / Hill, J.B. / Anderson, R.J. / Morris, J.C. / Rohatgi, A. / O'Mahony, G. / Grotli, M. / Danel, F. / Page, M.G.P. / Hartlein, M. / ...Authors: Sukuru, S.C.K. / Crepin, T. / Milev, Y. / Marsh, L.C. / Hill, J.B. / Anderson, R.J. / Morris, J.C. / Rohatgi, A. / O'Mahony, G. / Grotli, M. / Danel, F. / Page, M.G.P. / Hartlein, M. / Cusack, S. / Kron, M.A. / Kuhn, L.A.
History
DepositionJun 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASPARAGINYL-TRNA SYNTHETASE, CYTOPLASMIC
B: ASPARAGINYL-TRNA SYNTHETASE, CYTOPLASMIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1787
Polymers100,1142
Non-polymers1,0645
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-46.9 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.510, 125.700, 144.268
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 ASPARAGINYL-TRNA SYNTHETASE, CYTOPLASMIC


Mass: 50057.098 Da / Num. of mol.: 2
Fragment: CATALYTICALLY ACTIVE FRAGMENT LACKING N- TERMINAL EXTENSION, RESIDUES 114-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BRUGIA MALAYI (agent of lymphatic filariasis)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8PWE4, leucine-tRNA ligase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NSS / 5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE / ASN-SA


Mass: 461.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21N8O8S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGLYCEROL (GOL): FROM CRYOPROTECTANT

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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: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 8.5
Details: 100MM HEPES PH8.5, 200MM NA-ACETATE, 14-16% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 71529 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.9 / % possible all: 69.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T. THERMOPHILUS ASPARAGINYL-TRNA SYNTHETASE

Resolution: 1.9→94.92 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.799 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25017 2136 3 %RANDOM
Rwork0.20231 ---
obs0.20378 69345 88.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.042 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--1.44 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→94.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 0 70 496 7526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227187
X-RAY DIFFRACTIONr_bond_other_d0.0010.024947
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.979734
X-RAY DIFFRACTIONr_angle_other_deg0.898311981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66923.722360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.695151238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8271558
X-RAY DIFFRACTIONr_chiral_restr0.0840.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021517
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6921.54292
X-RAY DIFFRACTIONr_mcbond_other0.1541.51735
X-RAY DIFFRACTIONr_mcangle_it1.26126934
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.82532895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9144.52800
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 117 -
Rwork0.355 3334 -
obs--58.76 %

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