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- PDB-3vqv: Crystal structure of the catalytic domain of pyrrolysyl-tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 3vqv
TitleCrystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AMPPNP (re-refined)
ComponentsPyrrolysine--tRNA ligase
KeywordsLIGASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / aminoacyl-tRNA synthetase / pyrrolysyl-tRNA synthetase / AMPPNP
Function / homology
Function and homology information


pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Pyrrolysyl-tRNA ligase / Pyrrolysyl-tRNA ligase, N-terminal / Helix hairpin bin / Pyrrolysyl-tRNA ligase, C-terminal / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...Pyrrolysyl-tRNA ligase / Pyrrolysyl-tRNA ligase, N-terminal / Helix hairpin bin / Pyrrolysyl-tRNA ligase, C-terminal / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / 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) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYanagisawa, T. / Sumida, T. / Ishii, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site
Authors: Yanagisawa, T. / Sumida, T. / Ishii, R. / Yokoyama, S.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase
Authors: Yanagisawa, T. / Ishii, R. / Fukunaga, R. / Kobayashi, T. / Sakamoto, K. / Yokoyama, S.
History
DepositionApr 1, 2012Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 2, 2013ID: 2ZCD
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 8, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8994
Polymers33,3441
Non-polymers5553
Water4,432246
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7988
Polymers66,6882
Non-polymers1,1106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area6890 Å2
ΔGint-55 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.876, 104.876, 70.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Pyrrolysine--tRNA ligase / Pyrrolysyl-tRNA synthetase / PylRS


Mass: 33344.164 Da / Num. of mol.: 1 / Mutation: E444G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: JCM9314 / Gene: pylS / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus
References: UniProt: Q8PWY1*PLUS, pyrrolysine-tRNAPyl ligase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS STRAIN OF SOURCE (METHANOSARCINA MAZEI JCM9314) DOES NOT ...A SEQUENCE DATABASE REFERENCE FOR THIS STRAIN OF SOURCE (METHANOSARCINA MAZEI JCM9314) DOES NOT CURRENTLY EXIST. THIS SEQUENCE CONTAINS 21 A.A. N-TERMINAL TAGS AND C-TERMINAL DOMAIN(RESIDUES 185-454) OF PYLRS. AND THIS PROTEIN IS E444G MUTANT.

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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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Na/Cacodylate, MgCl2, PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 34806 / % possible obs: 99.8 % / Redundancy: 8 % / Rsym value: 0.089
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.9 % / Rsym value: 0.45 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VQW

3vqw


Resolution: 1.9→42.07 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.4 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 1750 5 %RANDOM
Rwork0.18657 ---
obs0.1882 33041 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.945 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.35 Å20 Å2
2---0.7 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 33 246 2374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222170
X-RAY DIFFRACTIONr_angle_refined_deg1.7062.012924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63723.925107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91615406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4861519
X-RAY DIFFRACTIONr_chiral_restr0.120.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021621
X-RAY DIFFRACTIONr_nbd_refined0.2250.2945
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21468
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.217
X-RAY DIFFRACTIONr_mcbond_it1.1861.51322
X-RAY DIFFRACTIONr_mcangle_it2.0822074
X-RAY DIFFRACTIONr_scbond_it2.9253953
X-RAY DIFFRACTIONr_scangle_it4.7834.5850
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 124 -
Rwork0.307 2449 -
obs--100 %

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