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- PDB-4bwa: PylRS Y306G, Y384F, I405R mutant in complex with adenylated norbornene -

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Basic information

Entry
Database: PDB / ID: 4bwa
TitlePylRS Y306G, Y384F, I405R mutant in complex with adenylated norbornene
ComponentsPYRROLYSINE--TRNA LIGASE
KeywordsLIGASE
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
Adenylated Norbornene / DI(HYDROXYETHYL)ETHER / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSchneider, S. / Vrabel, M. / Gattner, M.J. / Fluegel, V. / Lopez-Carillo, V. / Carell, T.
CitationJournal: Chem.Bio.Chem. / Year: 2013
Title: Structural Insights Into Incorporation of Norbornene Amino Acids for Click Modification of Proteins
Authors: Schneider, S. / Gattner, M.J. / Vrabel, M. / Flugel, V. / Lopez-Carrillo, V. / Prill, S. / Carell, T.
History
DepositionJul 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Dec 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)34,2186
Polymers33,3381
Non-polymers8805
Water59433
1
A: PYRROLYSINE--TRNA LIGASE
hetero molecules

A: PYRROLYSINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,43712
Polymers66,6762
Non-polymers1,76010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_785-x+2,-y+3,z1
Buried area6110 Å2
ΔGint-3.3 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.800, 104.800, 72.860
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: 33338.137 Da / Num. of mol.: 1 / Fragment: SYNTHETASE DOMAIN, RESIDUES 185-454 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA MAZEI (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase

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Non-polymers , 5 types, 38 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-N0B / Adenylated Norbornene


Mass: 625.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H36N7O10P
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.53 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM ACETATE, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.45→45.38 Å / Num. obs: 17790 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 10.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.4
Reflection shellResolution: 2.45→2.64 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BW9

4bw9


Resolution: 2.45→45.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.557 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21369 834 4.9 %RANDOM
Rwork0.18281 ---
obs0.18441 16038 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: 62.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å2-1.56 Å20 Å2
2---1.56 Å20 Å2
3---5.07 Å2
Refinement stepCycle: LAST / Resolution: 2.45→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 59 33 2169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022174
X-RAY DIFFRACTIONr_bond_other_d0.0040.022087
X-RAY DIFFRACTIONr_angle_refined_deg1.4752.0152927
X-RAY DIFFRACTIONr_angle_other_deg0.9653.0084809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4455257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81823.846104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97115385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.11519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212394
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
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_it2.2533.7561037
X-RAY DIFFRACTIONr_mcbond_other2.253.7551036
X-RAY DIFFRACTIONr_mcangle_it3.6945.6171291
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5184.0081137
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0435.9271637
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: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 73 -
Rwork0.277 1150 -
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)
17.03640.19250.38434.86271.39295.92190.4635-0.4147-0.38870.496-0.3084-0.60840.15080.3145-0.15510.1764-0.0389-0.09530.1448-0.06110.451224.2919102.5135-8.3078
24.3604-1.66236.27370.6596-2.42389.09130.70771.5537-0.1988-0.0842-0.56350.03340.74842.3246-0.14421.42540.2071-0.3351.12330.07280.709727.311899.77480.3115
31.8043-2.8656-2.025712.07057.40265.168-0.1906-0.0303-0.37551.17010.32190.21370.71580.1542-0.13130.274-0.0733-0.02820.11610.00650.309617.1487108.63991.556
42.59060.50060.33885.04030.12.99210.03430.26740.1283-0.23170.1105-0.3086-0.11010.1303-0.14480.0301-0.03310.03450.1005-0.00890.078134.4914138.0336-4.4051
521.931216.779914.144113.015710.95589.2239-0.45011.1241-0.19320.07220.526-0.01460.02940.5064-0.07591.064-0.35470.52810.9880.06990.694742.026134.6897-27.5741
63.43341.61221.63914.16542.1164.2937-0.12060.5346-0.0969-0.59730.2704-0.3903-0.11180.3105-0.14980.1617-0.07630.10080.19080.00020.116837.3879141.2494-11.1241
78.2658-8.43956.931326.0576-6.309215.06520.3790.77590.0482-0.6196-0.8438-1.40870.92480.81520.46480.233-0.0080.10210.2489-0.0950.298634.9824122.0222-13.5132
82.49010.18250.64142.5424-0.71781.8930.08020.2329-0.1924-0.2638-0.0386-0.73840.1490.2892-0.04160.0726-0.00710.04090.1912-0.05780.387447.0984131.1875-1.4521
92.79021.4469-0.17563.4008-0.31431.51610.02730.2618-0.4098-0.23520.0596-0.47590.10620.0888-0.08690.0797-0.01670.00840.0974-0.07950.155834.8764127.515-5.6502
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A187 - 205
2X-RAY DIFFRACTION2A206 - 212
3X-RAY DIFFRACTION3A213 - 239
4X-RAY DIFFRACTION4A240 - 278
5X-RAY DIFFRACTION5A279 - 286
6X-RAY DIFFRACTION6A287 - 335
7X-RAY DIFFRACTION7A336 - 340
8X-RAY DIFFRACTION8A341 - 406
9X-RAY DIFFRACTION9A407 - 454

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