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- PDB-3p0j: Leishmania major Tyrosyl-tRNA synthetase in complex with tyrosino... -

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Basic information

Entry
Database: PDB / ID: 3p0j
TitleLeishmania major Tyrosyl-tRNA synthetase in complex with tyrosinol, triclinic crystal form 1
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / aminoacyl-tRNA synthetase / tRNA ligase / aaRS / TyrRS / pseudodimer / translation / ATP-binding / nucleotide-binding / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ciliary plasm / ATP binding / cytoplasm
Similarity search - Function
: / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...: / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-[(2S)-2-amino-3-hydroxypropyl]phenol / tyrosine--tRNA ligase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.89 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Double-Length Tyrosyl-tRNA Synthetase from the Eukaryote Leishmania major Forms an Intrinsically Asymmetric Pseudo-Dimer.
Authors: Larson, E.T. / Kim, J.E. / Castaneda, L.J. / Napuli, A.J. / Zhang, Z. / Fan, E. / Zucker, F.H. / Verlinde, C.L. / Buckner, F.S. / Van Voorhis, W.C. / Hol, W.G. / Merritt, E.A.
History
DepositionSep 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms ..._chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-tRNA synthetase
B: Tyrosyl-tRNA synthetase
C: Tyrosyl-tRNA synthetase
D: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,00410
Polymers304,2904
Non-polymers7156
Water00
1
A: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2633
Polymers76,0721
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2402
Polymers76,0721
Non-polymers1671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2633
Polymers76,0721
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2402
Polymers76,0721
Non-polymers1671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.519, 111.934, 141.043
Angle α, β, γ (deg.)74.47, 80.83, 77.13
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12C
22A
13B
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 39
2114B1 - 39
3114C1 - 39
4114D1 - 39
1216A40 - 43
2216B40 - 43
3216C40 - 43
4216D40 - 43
1314A44 - 71
2314B44 - 71
3314C44 - 71
4314D44 - 71
1416A91 - 104
2416B91 - 104
3416C91 - 104
4416D91 - 104
1514A105 - 145
2514B105 - 145
3514C105 - 145
4514D105 - 145
1614A159 - 220
2614B159 - 220
3614C159 - 220
4614D159 - 220
1716A221 - 231
2716B221 - 231
3716C221 - 231
4716D221 - 231
1814A232 - 246
2814B232 - 246
3814C232 - 246
4814D232 - 246
1916A247 - 254
2916B247 - 254
3916C247 - 254
4916D247 - 254
11014A255 - 291
21014B255 - 291
31014C255 - 291
41014D255 - 291
11116A292 - 297
21116B292 - 297
31116C292 - 297
41116D292 - 297
11214A298 - 334
21214B298 - 334
31214C298 - 334
41214D298 - 334
11316A335 - 339
21316B335 - 339
31316C335 - 339
41316D335 - 339
11416A340 - 353
21416B340 - 353
31416C340 - 353
41416D340 - 353
11514A369 - 543
21514B369 - 543
31514C369 - 543
41514D369 - 543
11616A544 - 553
21616B544 - 553
31616C544 - 553
41616D544 - 553
11714A563 - 610
21714B563 - 610
31714C563 - 610
41714D563 - 610
11816A611 - 638
21816B611 - 638
31816C611 - 638
41816D611 - 638
11914A639 - 680
21914B639 - 680
31914C639 - 680
41914D639 - 680
1124C72 - 90
2124A72 - 90
1226C154 - 158
2226A154 - 158
1134B72 - 90
2134D72 - 90
1234B146 - 158
2234D146 - 158

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Tyrosyl-tRNA synthetase


Mass: 76072.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF14.1370 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4QFJ7, tyrosine-tRNA ligase
#2: Chemical
ChemComp-TYE / 4-[(2S)-2-amino-3-hydroxypropyl]phenol / tyrosinol / bound form of TYROSINAL


Type: L-peptide linking / Mass: 167.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13NO2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1:1:0.5 native protein solution (14 mg/ml LmTyrRS in MSGPP buffer containing 1 mM TCEP and 10 mM tyrosinol): well solutionn (16% PEG 3350, 0.2 M potassium formate pH 7.5): seed stock (1:100 ...Details: 1:1:0.5 native protein solution (14 mg/ml LmTyrRS in MSGPP buffer containing 1 mM TCEP and 10 mM tyrosinol): well solutionn (16% PEG 3350, 0.2 M potassium formate pH 7.5): seed stock (1:100 dilution in SGPP buffer); cryoprotected by quick soak in 15% ethylene glycol, 18.75% PEG 3350, 187.5 mM potassium formate pH 7.5, 10mM tyrosinol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 18, 2009
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionAv R equivalents: 0.093 / Number: 260725
ReflectionResolution: 2.89→135.13 Å / Num. obs: 72441 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.118
Reflection shellResolution: 2.89→3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 1.063 / Rsym value: 0 / % possible all: 97.9
Cell measurementReflection used: 260725

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.33 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.89 Å47.57 Å
Translation2.89 Å47.57 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.5.0110refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P0H

3p0h


Resolution: 2.89→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.221 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 65.028 / SU ML: 0.526 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.293 3649 5 %RANDOM
Rwork0.2438 ---
obs0.2462 72441 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 119.85 Å2 / Biso mean: 143.308 Å2 / Biso min: 60 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å2-2.29 Å2-0.71 Å2
2---1.74 Å20.89 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19644 0 50 0 19694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02220031
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213341
X-RAY DIFFRACTIONr_angle_refined_deg1.051.96627141
X-RAY DIFFRACTIONr_angle_other_deg0.809332620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41352553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78224.57860
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15153458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.57115123
X-RAY DIFFRACTIONr_chiral_restr0.0570.23134
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023807
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A5863MEDIUM POSITIONAL0.450.5
12B5863MEDIUM POSITIONAL0.460.5
13C5863MEDIUM POSITIONAL0.370.5
14D5863MEDIUM POSITIONAL0.370.5
11A892LOOSE POSITIONAL1.135
12B892LOOSE POSITIONAL1.225
13C892LOOSE POSITIONAL0.655
14D892LOOSE POSITIONAL0.545
21C251MEDIUM POSITIONAL0.360.5
21C47LOOSE POSITIONAL1.485
31B358MEDIUM POSITIONAL0.640.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-2.9610.4022450.3764671541290.835
2.961-3.0420.3992740.364989537597.916
3.042-3.130.4252630.3294792514798.213
3.13-3.2260.3712530.3164710504998.297
3.226-3.3320.3432150.2954581487198.46
3.332-3.4490.3332320.2844405471298.408
3.449-3.5790.3122160.2734311458898.67
3.579-3.7250.3042110.2654069433398.777
3.725-3.8910.3011930.2473975422898.581
3.891-4.0810.2842180.2343762402398.931
4.081-4.3010.281930.223562379998.842
4.301-4.5620.2522000.23380361699.004
4.562-4.8760.2361790.1943193340699.002
4.876-5.2660.271620.2152963316198.861
5.266-5.7680.31450.2392741291499.039
5.768-6.4470.3231210.2712482262099.351
6.447-7.4420.291120.2312177230999.134
7.442-9.1080.2311000.1821832194599.332
9.108-12.8510.215750.1751440152799.214
12.851-135.1250.301420.28475783595.689
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)
13.21981.9431.92353.8010.57451.7628-0.0685-0.4433-0.1353-0.29070.1386-0.12680.0519-0.0447-0.07010.3537-0.1010.17410.33940.00630.412128.8542.30280.884
22.24142.69431.45576.76522.51683.258-0.31470.12020.2702-1.13040.41940.8810.1699-0.1799-0.10470.6988-0.2023-0.36220.25130.23640.7094-3.7777.64860.881
32.63650.5664-1.48274.62290.27073.4405-0.35580.13220.3958-1.13180.39581.2764-0.4143-0.3717-0.040.9974-0.2318-0.45050.17610.10550.769910.35868.20662.896
44.67690.7536-1.74482.74570.293.5627-0.59160.7438-0.172-1.06630.4632-0.6032-0.16250.39530.12842.5147-0.7950.15250.6923-0.04960.475142.28668.70534.92
52.84810.06293.18171.69540.13563.99890.1759-0.7745-0.62460.49350.183-0.14990.2515-0.1956-0.35890.8502-0.22-0.10561.40480.44110.799425.115-8.06211.745
61.29750.19331.08961.50160.21336.46170.068-0.3137-0.4066-0.1272-0.05740.02210.7218-0.2796-0.01060.7654-0.2814-0.02330.80410.33030.9446-7.35-25.131-23.531
74.04220.5258-2.46413.2128-0.66223.28210.2127-1.21410.53370.74820.11530.4201-0.6210.1034-0.3281.0186-0.17680.08961.6039-0.11260.56615.99322.7712.514
82.68921.6172-1.55142.9318-1.38064.3065-0.0739-0.11570.2643-0.09050.0935-0.4319-0.50790.2247-0.01961.0983-0.38140.06640.8885-0.15450.667939.66242.667-20.676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 356
2X-RAY DIFFRACTION1A701
3X-RAY DIFFRACTION2A368 - 680
4X-RAY DIFFRACTION3B-1 - 355
5X-RAY DIFFRACTION3B701
6X-RAY DIFFRACTION4B360 - 679
7X-RAY DIFFRACTION5C-1 - 354
8X-RAY DIFFRACTION5C701
9X-RAY DIFFRACTION6C361 - 680
10X-RAY DIFFRACTION7D-1 - 354
11X-RAY DIFFRACTION7D701
12X-RAY DIFFRACTION8D366 - 681

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