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- PDB-4q6g: Crystal Structure of the C-terminal domain of AcKRS-1 bound with ... -

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Basic information

Entry
Database: PDB / ID: 4q6g
TitleCrystal Structure of the C-terminal domain of AcKRS-1 bound with N-acetyl-lysine and ADPNP
ComponentsPyrrolysine--tRNA ligase
KeywordsLIGASE / tRNA synthetase / tRNA / amino acids
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
N(6)-ACETYLLYSINE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsEiler, D.R. / Kavran, J. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.
Authors: Guo, L.T. / Wang, Y.S. / Nakamura, A. / Eiler, D. / Kavran, J.M. / Wong, M. / Kiessling, L.L. / Steitz, T.A. / O'Donoghue, P. / Soll, D.
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Sep 20, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8799
Polymers30,8121
Non-polymers1,0678
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.031, 105.031, 70.731
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 / AcKRS-1 / Pyrrolysine--tRNA(Pyl) ligase / Pyrrolysyl-tRNA synthetase / PylRS


Mass: 30812.246 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 188-454) / Mutation: L226V,L270I,Y271F,L274A,C313F,S382M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: pylS, MM_1445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PWY1, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ALY / N(6)-ACETYLLYSINE


Type: L-peptide linking / Mass: 188.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBIOCHEMICAL EVIDENCE SUGGESTS THAT THE ACETYL END OF LIGAND D ALY 2005 MAY NOT BE AS WELL-ORDERED ...BIOCHEMICAL EVIDENCE SUGGESTS THAT THE ACETYL END OF LIGAND D ALY 2005 MAY NOT BE AS WELL-ORDERED AS THE REST OF THE LIGAND.

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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: 3.66 Å3/Da / Density % sol: 66.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Tris, pH 8.0, 23% PEG2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2008
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.248→90.909 Å / Num. all: 21278 / Num. obs: 21010 / % possible obs: 98.7 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 7.5 % / Rsym value: 0.048 / Net I/σ(I): 41.2
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.248-2.335.32.60.538190.6
2.33-2.42197.5
2.42-2.53199.7
2.53-2.671100
2.67-2.831100
2.83-3.051100
3.05-3.361100
3.36-3.851100
3.85-4.851100
4.85-501100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q7G

2q7g


Resolution: 2.25→90.909 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.679 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21443 1079 5.1 %RANDOM
Rwork0.18593 ---
obs0.18737 19912 98.66 %-
all-21010 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.752 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0.57 Å2-0 Å2
2---1.14 Å20 Å2
3---3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→90.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 68 106 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192338
X-RAY DIFFRACTIONr_bond_other_d0.0030.022262
X-RAY DIFFRACTIONr_angle_refined_deg1.0922.0123161
X-RAY DIFFRACTIONr_angle_other_deg0.68435236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49623.947114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26115432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9811520
X-RAY DIFFRACTIONr_chiral_restr0.060.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
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_it2.7846.021094
X-RAY DIFFRACTIONr_mcbond_other2.7786.0181090
X-RAY DIFFRACTIONr_mcangle_it4.819.0141370
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6586.231244
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.248→2.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 73 -
Rwork0.26 1320 -
obs--88.39 %

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