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- PDB-4ch5: Structure of pyrrolysyl-tRNA synthetase in complex with adenylate... -

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Basic information

Entry
Database: PDB / ID: 4ch5
TitleStructure of pyrrolysyl-tRNA synthetase in complex with adenylated propionyl 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
PYROPHOSPHATE 2- / Chem-YLP / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Mar 4, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Dec 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 / 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_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)34,4589
Polymers33,4161
Non-polymers1,0428
Water1,60389
1
A: PYRROLYSINE--TRNA LIGASE
hetero molecules

A: PYRROLYSINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,91718
Polymers66,8322
Non-polymers2,08416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_785-x+2,-y+3,z1
Buried area7380 Å2
ΔGint-9 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.376, 105.376, 70.801
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 97 molecules

#2: Chemical ChemComp-YLP / (S)-2-amino-6-propionamidohexanoic(((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride


Mass: 531.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30N7O9P
#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: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.78 Å3/Da / Density % sol: 67.5 % / Description: NONE
Crystal growpH: 7.4 / Details: 0.1 M LIAC, 14% 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: Apr 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42.3 Å / Num. obs: 22651 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 10.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.96 / % possible all: 96.9

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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: 2.2→42.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU B: 6.877 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES 380-383 DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.18949 1159 5.1 %RANDOM
Rwork0.17371 ---
obs0.17453 21491 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.27 Å20 Å2
2---0.27 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 66 89 2244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192227
X-RAY DIFFRACTIONr_bond_other_d0.0010.022128
X-RAY DIFFRACTIONr_angle_refined_deg1.4392.0133006
X-RAY DIFFRACTIONr_angle_other_deg0.75534895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6265271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62423.491106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22315392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9581521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02507
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_it2.0473.0811063
X-RAY DIFFRACTIONr_mcbond_other2.0453.0811063
X-RAY DIFFRACTIONr_mcangle_it3.4024.5941326
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5383.1971164
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: 2.204→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 94 -
Rwork0.238 1499 -
obs--95.79 %
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)
16.10560.8894-0.5927.51073.33475.15750.2875-0.0718-0.40630.3511-0.0289-0.58250.30920.5459-0.25870.10090.0189-0.0980.08990.01040.224325.0025103.8991-7.3101
22.4231-2.0366-1.418714.78488.13758.70.0084-0.2051-0.20041.3674-0.08570.35741.051-0.03870.07720.2249-0.0753-0.04670.06140.06070.080318.5091104.1949-0.8263
310.08236.8520.24054.76080.40090.68350.1525-0.0658-0.23350.2599-0.043-0.18280.25760.0882-0.10950.2876-0.0463-0.01120.20090.02760.225425.2449128.07125.7452
41.4750.0353-0.23461.9347-0.04293.270.03210.0960.041-0.13650.034-0.2105-0.06150.1808-0.06620.0767-0.08040.00970.1091-0.00140.115936.8736143.2444-8.6885
513.8761-1.1249-3.97579.8042-1.15652.74740.3110.6134-0.2074-0.9794-0.1359-0.6288-0.1090.2923-0.1750.3452-0.08050.1060.2993-0.1070.126537.7167135.5761-23.8488
61.92911.07170.53562.43940.59411.6815-0.10610.1791-0.0721-0.17740.1155-0.2651-0.07270.1704-0.00940.0572-0.07540.01480.118-0.00950.082137.5737140.6279-9.4719
77.99061.84350.79891.0781-0.60562.09170.0205-0.0101-0.11170.0914-0.0941-0.2467-0.19240.50680.07370.0829-0.0557-0.02260.2088-0.0080.147548.8843139.25790.148
84.07481.0056-0.68275.1808-1.98915.49960.03050.3266-0.2662-0.1907-0.063-0.50470.15620.2260.03250.0447-0.0017-0.05750.17-0.0060.215948.1388128.94451.5778
91.59990.5580.68165.3809-2.14831.66510.0410.35410.0064-0.3519-0.2226-0.3876-0.00820.3410.18160.2493-0.00860.06170.3475-0.03620.26148.7174136.3694-8.8433
102.92391.36910.65132.14630.03521.3365-0.00360.1365-0.2741-0.00590.1073-0.15660.12660.0581-0.10370.0467-0.0238-0.00540.047-0.02760.039332.922125.2517-4.1621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A188 - 207
2X-RAY DIFFRACTION2A212 - 231
3X-RAY DIFFRACTION3A232 - 253
4X-RAY DIFFRACTION4A254 - 277
5X-RAY DIFFRACTION5A278 - 292
6X-RAY DIFFRACTION6A293 - 343
7X-RAY DIFFRACTION7A344 - 360
8X-RAY DIFFRACTION8A361 - 389
9X-RAY DIFFRACTION9A390 - 413
10X-RAY DIFFRACTION10A414 - 454

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