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- PDB-4ch6: Structure of pyrrolysyl-tRNA synthetase in complex with adenylate... -

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Basic information

Entry
Database: PDB / ID: 4ch6
TitleStructure of pyrrolysyl-tRNA synthetase in complex with adenylated propargyloxycarbonyl lysine
ComponentsPYRROLYSINE--TRNA LIGASE
KeywordsLIGASE / NON-NATURAL AMINO ACID / PYRROLYSINE
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
Chem-YLA / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFluegel, V. / Vrabel, M. / Schneider, S.
CitationJournal: Plos One / Year: 2014
Title: Structural Basis for the Site-Specific Incorporation of Lysine Derivatives Into Proteins.
Authors: Flugel, V. / Vrabel, M. / Schneider, S.
History
DepositionNov 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_conn.ptnr2_label_seq_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)34,3088
Polymers33,4161
Non-polymers8927
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.933, 104.933, 70.964
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 / PYRROLYSINE--TRNA(PYL) LIGASE / PYRROLYSYL-TRNA SYNTHETASE / PYLRS


Mass: 33416.227 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 185-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA MAZEI (archaea) / Strain: GO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase
#2: Chemical ChemComp-YLA / (S)-2-amino-6-(((prop-2-yn-1-yloxy)carbonyl)amino)hexanoic (((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric)anhydride


Mass: 557.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N7O10P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 21 AMINO ACIDS DISORDERED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67.3 % / Description: NONE
Crystal growpH: 7.4 / Details: 0.1 M LIAC, 12% PEG3350, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→38.29 Å / Num. obs: 28018 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 9.7 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 45.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.29 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BWA

4bwa


Resolution: 2.05→38.29 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 5.792 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18474 1408 5 %RANDOM
Rwork0.17369 ---
obs0.17426 26610 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.55 Å20 Å2
2---0.55 Å20 Å2
3---1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.05→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 59 117 2265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192219
X-RAY DIFFRACTIONr_bond_other_d0.0010.022121
X-RAY DIFFRACTIONr_angle_refined_deg1.4972.0092992
X-RAY DIFFRACTIONr_angle_other_deg0.77234877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33523.491106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1315390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2931521
X-RAY DIFFRACTIONr_chiral_restr0.0850.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02506
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_it2.33.5851062
X-RAY DIFFRACTIONr_mcbond_other2.2973.5851062
X-RAY DIFFRACTIONr_mcangle_it3.5315.3371323
X-RAY DIFFRACTIONr_mcangle_other3.5315.3421324
X-RAY DIFFRACTIONr_scbond_it2.683.7981157
X-RAY DIFFRACTIONr_scbond_other2.683.7981157
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0935.6041665
X-RAY DIFFRACTIONr_long_range_B_refined7.99528.452506
X-RAY DIFFRACTIONr_long_range_B_other7.99428.4642507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 113 -
Rwork0.303 1956 -
obs--99.76 %
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)
15.17760.7967-2.21397.99772.26144.09750.3175-0.2597-0.3110.5555-0.1398-0.78770.32860.5549-0.17770.11930.0243-0.11720.12250.02130.295524.6834103.4398-7.5662
20.653-1.29821.17532.6-2.35952.14270.20870.29590.2759-0.4539-0.6526-0.50350.42050.60870.44390.41360.0998-0.13360.40280.00430.44326.654997.65920.175
30.6961-2.8061-1.612312.157.24515.3436-0.1737-0.1024-0.13811.11670.13970.45740.8158-0.01940.0340.2431-0.1055-0.00880.10880.06390.165117.3494109.21111.6442
48.40464.42181.9764.65580.9151.9067-0.0384-0.0273-0.2150.14510.0624-0.18810.0680.0127-0.0240.0391-0.0359-0.01110.08720.00770.073330.517131.54724.2949
51.75710.02260.27231.61760.12892.3361-0.10350.10740.0991-0.21630.0659-0.2587-0.14720.21640.03770.1022-0.11040.02350.14480.00170.147936.812142.5265-9.8472
61.5940.31170.11872.07090.21591.6856-0.16090.23420.0401-0.34550.1631-0.2504-0.13090.2609-0.00220.1131-0.11690.03390.1648-0.00950.127538.0811142.0727-11.9366
73.50161.21250.9621.7141-0.0991.5699-0.13530.1115-0.1748-0.15250.0847-0.2506-0.01950.26270.05060.0429-0.0580.050.1385-0.03090.124342.342133.286-6.0099
82.02550.3420.55193.9165-0.99752.21280.00020.2178-0.2912-0.27910.0252-0.47690.2050.2329-0.02540.0394-0.0118-0.0040.1652-0.02350.237947.6797127.1563-0.0708
91.93590.74650.40532.1343-0.14281.2703-0.04640.1928-0.17-0.13670.0765-0.2625-0.04020.166-0.03010.0741-0.04520.02920.0891-0.04320.089437.3836129.7189-5.9472
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A188 - 206
2X-RAY DIFFRACTION2A207 - 213
3X-RAY DIFFRACTION3A214 - 239
4X-RAY DIFFRACTION4A240 - 254
5X-RAY DIFFRACTION5A255 - 278
6X-RAY DIFFRACTION6A279 - 330
7X-RAY DIFFRACTION7A331 - 359
8X-RAY DIFFRACTION8A360 - 399
9X-RAY DIFFRACTION9A400 - 454

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