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- PDB-4ch4: Structure of pyrrolysyl-tRNA synthetase in complex with adenylate... -

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Basic information

Entry
Database: PDB / ID: 4ch4
TitleStructure of pyrrolysyl-tRNA synthetase in complex with adenylated crotonyl 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-YLC / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 26, 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 / _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)34,2948
Polymers33,4161
Non-polymers8787
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.045, 105.045, 71.771
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-YLC / 5'-O-[({(2R)-2-amino-6-[(2E)-but-2-enoylamino]hexanoyl}oxy)phosphinato]adenosine


Mass: 543.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N7O9P
#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.: 169 / 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: 3.82 Å3/Da / Density % sol: 67.86 % / Description: NONE
Crystal growpH: 7.4 / Details: 0.1 M LIAC, 10% 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: 2.16→42.42 Å / Num. obs: 24308 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 10.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.19
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.53 / % possible all: 100

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Processing

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

4bwa


Resolution: 2.16→42.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.466 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 1206 5 %RANDOM
Rwork0.16536 ---
obs0.16749 23100 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.273 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.47 Å20 Å2
2---0.47 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.16→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 58 169 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192180
X-RAY DIFFRACTIONr_bond_other_d0.0010.022088
X-RAY DIFFRACTIONr_angle_refined_deg1.462.012939
X-RAY DIFFRACTIONr_angle_other_deg0.76834799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13623.558104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78415381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6331520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
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_it1.3612.1531044
X-RAY DIFFRACTIONr_mcbond_other1.3612.1531044
X-RAY DIFFRACTIONr_mcangle_it2.1813.2151300
X-RAY DIFFRACTIONr_mcangle_other2.183.2131301
X-RAY DIFFRACTIONr_scbond_it1.8252.2141136
X-RAY DIFFRACTIONr_scbond_other1.8252.2121137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.793.2391636
X-RAY DIFFRACTIONr_long_range_B_refined8.04817.3972505
X-RAY DIFFRACTIONr_long_range_B_other8.04617.3922506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 73 -
Rwork0.236 1706 -
obs--100 %
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)
16.0032-0.5335-1.80998.2731-4.75649.36170.20070.2001-0.3282-0.44750.180.61130.3185-0.7218-0.38070.1026-0.021-0.11090.0741-0.00510.2222-24.7399103.52119.6619
23.2001-2.51360.79492.0951-0.60810.21640.88931.05920.9937-0.8578-1.0267-0.90810.31070.20660.13740.99910.1780.23180.83850.33630.931-27.208498.11182.823
31.49093.0928-1.984613.2056-8.38627.3706-0.12610.1678-0.0781-0.99540.17-0.23050.7483-0.2121-0.0440.15550.0253-0.02210.065-0.04810.0955-17.8141108.84430.2437
410.3309-5.87041.16973.346-0.65840.19380.1868-0.002-0.1606-0.1464-0.06290.06630.1228-0.0516-0.12380.31120.0139-0.0330.2816-0.0010.281-28.6533130.8252-2.7533
51.7203-0.33210.00392.1722-0.19974.1665-0.0767-0.12320.06280.19950.02970.2187-0.0792-0.05780.04690.08140.05930.02270.08680.00850.1431-36.7531142.816610.6505
610.8916-3.5224-4.07899.8019-0.42713.16460.4636-0.751-0.19940.9552-0.15650.9525-0.2913-0.2572-0.30710.44120.00540.12210.44210.07320.2019-37.5123135.136825.7902
71.486-0.90260.17252.4571-0.54481.1294-0.0938-0.09910.07280.13720.12930.199-0.1585-0.1601-0.03560.0490.05490.01410.10490.01680.102-38.4813144.64879.8813
85.4768-0.3505-1.78879.3448-0.05496.56670.1173-0.5199-0.51620.73970.0650.79150.4867-0.2704-0.18230.18240.020.04240.17660.06770.1933-34.2352126.160715.4444
94.8776-2.8095-0.22475.59520.41281.17230.048-0.0669-0.0345-0.3582-0.15140.3202-0.0758-0.34330.10340.05820.0375-0.02530.16350.02060.1317-49.6987139.08490.9272
102.2461-0.13711.25443.42711.34462.93860.0903-0.2811-0.16130.2361-0.04170.38420.2417-0.1679-0.04860.07450.0078-0.0350.13060.02890.2206-46.4443126.41161.6053
111.92031.93280.69615.58542.1791.01270.0297-0.38510.14450.5199-0.20490.59060.1075-0.34020.17520.28350.15110.07280.6128-0.00750.3709-51.0002144.936713.4898
122.5596-1.26610.73811.8984-0.26241.14490.0394-0.0903-0.2906-0.01670.07680.18910.1734-0.0623-0.11620.04320.0061-0.01130.04290.03260.0748-32.5325124.44845.7406
139.06538.7250.0088.3990.00830.0007-0.0979-0.29271.213-0.2961-0.09361.1785-0.0167-0.01620.19150.6990.31140.10050.69650.09530.7459-42.2369132.850111.1945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A187 - 206
2X-RAY DIFFRACTION2A207 - 213
3X-RAY DIFFRACTION3A214 - 238
4X-RAY DIFFRACTION4A239 - 253
5X-RAY DIFFRACTION5A254 - 277
6X-RAY DIFFRACTION6A278 - 292
7X-RAY DIFFRACTION7A293 - 330
8X-RAY DIFFRACTION8A331 - 344
9X-RAY DIFFRACTION9A345 - 361
10X-RAY DIFFRACTION10A362 - 399
11X-RAY DIFFRACTION11A400 - 414
12X-RAY DIFFRACTION12A415 - 454
13X-RAY DIFFRACTION13A500

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