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- PDB-3vqw: Crystal structure of the SeMet substituted catalytic domain of py... -

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Basic information

Entry
Database: PDB / ID: 3vqw
TitleCrystal structure of the SeMet substituted catalytic domain of pyrrolysyl-tRNA synthetase
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 / MAD / Resolution: 2.4 Å
AuthorsYanagisawa, T. / Sumida, T. / Ishii, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: 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.
History
DepositionApr 1, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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.pdbx_leaving_atom_flag / _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)34,2744
Polymers33,7191
Non-polymers5553
Water2,576143
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5488
Polymers67,4392
Non-polymers1,1106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area6780 Å2
ΔGint-60 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.091, 105.091, 70.629
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: 33719.324 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.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Na/Cacodylate, NaCl, MgSO4, PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9791, 0.9794, 0.9840
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 4, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.9841
ReflectionResolution: 2.4→50 Å / Num. obs: 17400 / % possible obs: 99.3 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.09
Reflection shellResolution: 2.4→2.44 Å / Rsym value: 0.411 / % possible all: 96.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SOLVEphasing
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→42.16 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2093308.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1726 9.9 %RANDOM
Rwork0.2 ---
obs0.2 17347 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2699 Å2 / ksol: 0.293082 e/Å3
Displacement parametersBiso mean: 45.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.12 Å24.72 Å20 Å2
2---5.12 Å20 Å2
3---10.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.4→42.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 33 143 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.88
X-RAY DIFFRACTIONc_mcbond_it5.711.5
X-RAY DIFFRACTIONc_mcangle_it7.922
X-RAY DIFFRACTIONc_scbond_it9.352
X-RAY DIFFRACTIONc_scangle_it11.532.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 285 10.3 %
Rwork0.37 2494 -
obs--95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4AMPPNP.paramAMPPNP.top

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