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- PDB-3rl6: Crystal structure of the archaeal asparagine synthetase A complex... -

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Basic information

Entry
Database: PDB / ID: 3rl6
TitleCrystal structure of the archaeal asparagine synthetase A complexed with L-Asparagine and Adenosine monophosphate
ComponentsArchaeal asparagine synthetase A
KeywordsLIGASE / AMP and Asn binding / seven stranded antiparallel 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
ADENOSINE MONOPHOSPHATE / ASPARAGINE / AsnS-like asparaginyl-tRNA synthetase related protein
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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: Archaeal asparagine synthetase A
B: Archaeal asparagine synthetase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2467
Polymers68,2632
Non-polymers9835
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-66 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.730, 60.900, 154.920
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 Archaeal asparagine synthetase A / 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) / Strain: GE5/Orsay / 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: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


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


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


Mass: 18.015 Da / Num. of mol.: 334 / 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: 39.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM Tris-HCl pH7, 0.2M NaCl, 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 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 131111 / Num. obs: 37794 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→50 Å / % possible all: 98.4

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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 / Resolution: 2→47.875 Å / SU ML: 0.21 / σ(F): 2.01 / Phase error: 19.04 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1989 5.26 %random
Rwork0.1694 ---
all0.172 37791 --
obs0.172 37791 98.38 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.41 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9504 Å2-0 Å20 Å2
2---0.7664 Å20 Å2
3---6.3382 Å2
Refinement stepCycle: LAST / Resolution: 2→47.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 65 334 5144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074931
X-RAY DIFFRACTIONf_angle_d1.0226655
X-RAY DIFFRACTIONf_dihedral_angle_d13.5581881
X-RAY DIFFRACTIONf_chiral_restr0.075694
X-RAY DIFFRACTIONf_plane_restr0.004851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28331360.2132560X-RAY DIFFRACTION100
2.05-2.10550.26751530.20392568X-RAY DIFFRACTION100
2.1055-2.16740.2651320.22563X-RAY DIFFRACTION100
2.1674-2.23740.24741450.18142534X-RAY DIFFRACTION100
2.2374-2.31730.19861380.17852540X-RAY DIFFRACTION100
2.3173-2.41010.2271520.172558X-RAY DIFFRACTION100
2.4101-2.51980.23091370.17642581X-RAY DIFFRACTION100
2.5198-2.65260.21011430.17712569X-RAY DIFFRACTION100
2.6526-2.81880.24221410.16342581X-RAY DIFFRACTION99
2.8188-3.03640.21271430.1742553X-RAY DIFFRACTION99
3.0364-3.34190.23481400.17112546X-RAY DIFFRACTION98
3.3419-3.82530.21051420.15292550X-RAY DIFFRACTION97
3.8253-4.81880.20271420.14062545X-RAY DIFFRACTION96
4.8188-47.88890.18441450.16662554X-RAY DIFFRACTION91
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)
10.0651-0.0028-0.01920.0102-0.01470.10050.0184-0.00570.02770.03880.01460.0063-0.0347-0.01560.00270.0371-0.02150.04720.064-0.02390.0705-21.79676.859125.1055
20.0325-0.0288-0.0040.0307-0.02180.1142-0.01280.04960.0175-0.0256-0.0312-0.03460.05110.00340.020.0369-0.00090.01090.03250.01020.0442-16.4314-3.626.8909
30.0114-0.0158-0.01230.0525-0.02470.0814-0.0334-0.0208-0.0140.0004-0.023-0.07080.02490.0556-0.05160.03480.02260.00790.02660.04360.1319-9.574-4.79055.2118
40.0135-0.01740.00320.0336-0.00360.01380.00030.00440.02450.0091-0.0138-0.0125-0.0127-0.0086-0.0619-0.04980.00250.0163-0.03550.00290.0383-23.40256.275810.7801
50.0526-0.05890.01150.0724-0.00150.0174-0.0040.01040.0353-0.01080.002-0.0326-0.01980.00220.01030.05480.02110.00420.02950.02760.1011-27.336820.76315.2017
60.0654-0.02940.02570.0179-0.01940.0425-0.0275-0.00770.07130.0047-0.0121-0.0221-0.02880.0109-0.1115-0.01730.0253-0.0302-0.0210.02020.048-21.386415.16320.8597
70.0308-0.00270.01110.0609-0.03770.0334-0.00290.00230.009-0.0355-0.0199-0.03150.02430.0127-0.09420.00850.00580.0038-0.0126-0.00090.0031-15.40972.07314.5108
80.05360.0333-0.04770.0928-0.09510.1332-0.0413-0.0347-0.03460.018-0.0486-0.08660.05760.086-0.21270.0617-0.0430.02220.02480.060.0255-15.8447-7.764620.7817
90.05580.03750.02250.0240.0060.0162-0.0105-0.0585-0.02830.0258-0.0267-0.02260.09210.0003-0.02550.1509-0.03940.09110.07210.0702-0.0447-20.6101-13.479828.2504
100.0432-0.00950.02960.00590.00180.0655-0.0229-0.0164-0.02050.0306-0.0135-0.01970.03930.0181-0.09760.2501-0.0318-0.00880.15540.1420.1129-19.2493-25.520335.7862
110.08940.0862-0.00660.1376-0.01630.1996-0.0056-0.137-0.03940.0626-0.1433-0.16250.04210.1759-0.32940.1699-0.0532-0.0340.12990.19420.045-11.0999-13.441330.2997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:32)
2X-RAY DIFFRACTION2chain 'A' and (resseq 33:52)
3X-RAY DIFFRACTION3chain 'A' and (resseq 53:85)
4X-RAY DIFFRACTION4chain 'A' and (resseq 86:148)
5X-RAY DIFFRACTION5chain 'A' and (resseq 149:169)
6X-RAY DIFFRACTION6chain 'A' and (resseq 170:213)
7X-RAY DIFFRACTION7chain 'A' and (resseq 214:294)
8X-RAY DIFFRACTION8chain 'B' and (resseq 1:85)
9X-RAY DIFFRACTION9chain 'B' and (resseq 86:148)
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:197)
11X-RAY DIFFRACTION11chain 'B' and (resseq 198:294)

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