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

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Basic information

Entry
Database: PDB / ID: 3reu
TitleCrystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid and Adenosine triphosphate
ComponentsAsnS-like asparaginyl-tRNA synthetase related protein
KeywordsLIGASE / ATP binding / Aspartic acid binding / 7 stranded anti parallel beta-sheet
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
ASPARTIC ACID / ADENOSINE-5'-TRIPHOSPHATE / AsnS-like asparaginyl-tRNA synthetase related protein
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_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)69,55611
Polymers68,2632
Non-polymers1,2939
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-112 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.470, 61.180, 156.940
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


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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.06 Å3/Da / Density % sol: 40.18 %
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: 1.9→50 Å / Num. obs: 44981 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.34
Reflection shellResolution: 1.9→2 Å / % possible all: 99.9

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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: 1.9→48.249 Å / SU ML: 0.23 / σ(F): 2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 1996 4.44 %random
Rwork0.1702 ---
all0.172 44981 --
obs0.172 44979 99.39 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.556 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.118 Å20 Å20 Å2
2--0.3109 Å20 Å2
3---5.7338 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 77 299 5158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074983
X-RAY DIFFRACTIONf_angle_d1.1256737
X-RAY DIFFRACTIONf_dihedral_angle_d13.4111916
X-RAY DIFFRACTIONf_chiral_restr0.078698
X-RAY DIFFRACTIONf_plane_restr0.004858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.3071330.24413051X-RAY DIFFRACTION100
1.9475-2.00020.31891420.21723025X-RAY DIFFRACTION100
2.0002-2.0590.26541400.20183054X-RAY DIFFRACTION100
2.059-2.12550.21991390.17553031X-RAY DIFFRACTION100
2.1255-2.20150.22471400.17613052X-RAY DIFFRACTION100
2.2015-2.28960.22731460.16873050X-RAY DIFFRACTION100
2.2896-2.39380.22021500.18643028X-RAY DIFFRACTION100
2.3938-2.520.2761370.18443072X-RAY DIFFRACTION100
2.52-2.67790.24691420.18613069X-RAY DIFFRACTION100
2.6779-2.88460.2331460.1823078X-RAY DIFFRACTION100
2.8846-3.17490.20271430.1813065X-RAY DIFFRACTION99
3.1749-3.63410.20021460.16083115X-RAY DIFFRACTION99
3.6341-4.57810.16121400.13663083X-RAY DIFFRACTION98
4.5781-48.2640.17151520.15533210X-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)
10.0012-0.00520.00190.0834-0.01740.0371-0.02110.0330.02120.04670.0381-0.02630.01550.0338-0.00950.04370.0135-0.0540.09490.01820.083221.8095-6.914125.2564
20.0038-0.0058-0.00230.0120.01290.0202-0.0427-0.0125-0.0331-0.0098-0.03410.06450.0105-0.01270.0316-0.0185-0.0213-0.00540.0998-0.02010.166914.69631.00827.6565
30.0087-0.00460.01630.01720.00840.0373-0.03980.0575-0.01270.0081-0.0165-0.00020.04390.04980.02960.00170.05290.00370.1014-0.01950.188528.3864-17.63148.5695
40.00710.01320.00690.030.01930.0249-0.06820.0668-0.0659-0.0001-0.01840.0551-0.02530.00790.0254-0.0823-0.00650.01280.0697-0.01370.075717.9061-5.64453.0005
50.0761-0.0235-0.05590.3587-0.04630.0635-0.0356-0.01060.00760.13530.01840.0589-0.07370.00130.01010.0957-0.0097-0.01770.06730.01190.066518.462810.065919.7825
60.0021-0.00110.00610.0042-0.00880.0406-0.0010.01590.00060.006-0.00620.0133-0.00630.0052-0.0010.06190.01730.06150.073-0.03190.03795.54752.877726.2278
70.0289-0.0235-0.01870.06960.04310.0227-0.009-0.07950.00370.08330.00070.0317-0.01340.03460.00170.19840.0028-0.05790.1245-0.02860.01520.725213.290228.5139
80.02050.00250.01850.0159-0.01160.029-0.01470.0191-0.0024-0.0460.0045-0.00120.02570.06660.00310.2560.00390.01290.1834-0.09720.095124.596226.655336.7207
90.0108-0.00560.0010.00360.00070.0023-0.0456-0.02920.00960.01640.00220.0069-0.0112-0.01380.02870.2562-0.02390.02190.1389-0.07230.042215.630124.12135.8077
100.04890.0198-0.01580.00910.01190.0395-0.0195-0.01840.00050.0204-0.01240.0288-0.0347-0.01340.00780.160.01660.09940.0337-0.0858-0.03489.213414.939538.2646
110.00970.00360.02780.01170.00620.0809-0.00940.0198-0.0055-0.01040.00460.0022-0.0353-0.01920.00110.2426-0.04960.11630.23240.05080.13830.65580.220636.9468
120.00570.00480.00420.00830.01140.02160.0034-0.00240.00230.0211-0.00240.0069-0.0165-0.0010.00090.0728-0.0029-0.0711-0.0184-0.0731-0.048719.168218.792417.023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:32)
2X-RAY DIFFRACTION2chain 'A' and (resseq 33:125)
3X-RAY DIFFRACTION3chain 'A' and (resseq 126:179)
4X-RAY DIFFRACTION4chain 'A' and (resseq 180:294)
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:65)
6X-RAY DIFFRACTION6chain 'B' and (resseq 66:85)
7X-RAY DIFFRACTION7chain 'B' and (resseq 86:148)
8X-RAY DIFFRACTION8chain 'B' and (resseq 149:169)
9X-RAY DIFFRACTION9chain 'B' and (resseq 170:197)
10X-RAY DIFFRACTION10chain 'B' and (resseq 198:239)
11X-RAY DIFFRACTION11chain 'B' and (resseq 240:257)
12X-RAY DIFFRACTION12chain 'B' and (resseq 258:294)

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