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- PDB-3hzr: Tryptophanyl-tRNA synthetase homolog from Entamoeba histolytica -

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Basic information

Entry
Database: PDB / ID: 3hzr
TitleTryptophanyl-tRNA synthetase homolog from Entamoeba histolytica
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / apo tRNA-ligase / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / 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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tryptophanyl-tRNA synthetase, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsArakaki, T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2011
Title: Crystal structures of three protozoan homologs of tryptophanyl-tRNA synthetase.
Authors: Merritt, E.A. / Arakaki, T.L. / Gillespie, R. / Napuli, A.J. / Kim, J.E. / Buckner, F.S. / Van Voorhis, W.C. / Verlinde, C.L. / Fan, E. / Zucker, F. / Hol, W.G.
History
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophanyl-tRNA synthetase
B: Tryptophanyl-tRNA synthetase
C: Tryptophanyl-tRNA synthetase
D: Tryptophanyl-tRNA synthetase
E: Tryptophanyl-tRNA synthetase
F: Tryptophanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)264,8486
Polymers264,8486
Non-polymers00
Water0
1
A: Tryptophanyl-tRNA synthetase
B: Tryptophanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)88,2832
Polymers88,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-21 kcal/mol
Surface area32160 Å2
MethodPISA
2
C: Tryptophanyl-tRNA synthetase
D: Tryptophanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)88,2832
Polymers88,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-23 kcal/mol
Surface area32190 Å2
MethodPISA
3
E: Tryptophanyl-tRNA synthetase
F: Tryptophanyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)88,2832
Polymers88,2832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-22 kcal/mol
Surface area32190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.200, 158.880, 100.280
Angle α, β, γ (deg.)90.000, 107.330, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 8 - 381 / Label seq-ID: 13 - 386

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
Tryptophanyl-tRNA synthetase


Mass: 44141.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: 58.m00157 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LUB5*PLUS

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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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.2 M Sodium Citrate, 20% PEG 3350, 1mM TCEP, 10 mM Zn, pH 7.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3→47.891 Å / Num. obs: 54415 / % possible obs: 97.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 85 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 5.609
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.163.10.72511679761.04698.8
3.16-3.353.21.22422575980.63998.7
3.35-3.593.22.12280171180.35698.5
3.59-3.873.23.62111165680.20898
3.87-4.243.25.41955960600.13497.8
4.24-4.743.27.71769554540.09297.4
4.74-5.483.38.91566148100.07796.9
5.48-6.713.39.11320240340.07596.3
6.71-9.493.313.41019531040.04595.5
9.49-48.623.313.7551016930.03793.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefmac_5.5.0089refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FOC

3foc


Resolution: 3→47.89 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 1 / SU B: 55.186 / SU ML: 0.433 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2753 5.1 %RANDOM
Rwork0.228 ---
obs0.229 54396 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.42 Å2 / Biso mean: 20.134 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-2.73 Å2
2---3.69 Å20 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 3→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17738 0 0 0 17738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02218104
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212074
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.95424504
X-RAY DIFFRACTIONr_angle_other_deg0.924329610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14452238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50825.012818
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.222153158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6711554
X-RAY DIFFRACTIONr_chiral_restr0.0720.22804
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0220042
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023660
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4964 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT POSITIONAL / Weight position: 0.05

Auth asym-IDRms dev position (Å)
A0.03
B0.03
C0.03
D0.03
E0.02
F0.03
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 (%)
3-3.0780.4011930.3773805406498.376
3.078-3.1620.3461820.3463748398398.669
3.162-3.2530.3121790.3133652387898.788
3.253-3.3530.3171890.2973563381098.478
3.353-3.4620.3151720.2913437366798.418
3.462-3.5830.2821980.2643277353498.331
3.583-3.7170.2821390.253217342398.043
3.717-3.8680.241610.2383032325997.975
3.868-4.0390.2611740.2252915315897.815
4.039-4.2340.2611500.222806302797.654
4.234-4.4620.2131640.1922639287897.394
4.462-4.730.2231510.1792498272697.175
4.73-5.0530.191330.1782343255596.908
5.053-5.4520.1981220.1982201239896.872
5.452-5.9650.3041030.2462002218896.207
5.965-6.6560.2671010.2441837201596.179
6.656-7.6610.255950.2071603177995.447
7.661-9.3240.203600.161380151295.238
9.324-12.9430.166570.1491054118094.153
12.943-47.8910.234300.29963471393.128
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)
11.74850.28220.01496.51860.36972.7224-0.1485-0.3127-0.45640.94990.4417-0.70420.88960.4529-0.29320.42220.2466-0.14480.32520.04020.27356.545412.80940.4388
22.2121-0.3554-0.57216.2597-0.03632.36560.0618-0.09210.5964-0.85620.3789-0.913-0.82490.5099-0.44070.4624-0.30860.26310.2863-0.14960.432513.558157.023917.9672
34.39781.57490.55664.52791.1812.20470.1697-0.1195-0.09270.2927-0.45331.58560.4485-0.47590.28360.0963-0.06760.07480.3746-0.19371.1199-40.052829.087139.6502
41.5870.96640.39365.4453.30163.2371-0.0092-0.31170.24551.07260.0266-0.11890.2850.1464-0.01740.39040.0677-0.03860.3509-0.0630.2383-7.939959.618262.5157
53.2741-2.0722-0.17744.52430.51872.70460.41670.43440.1405-1.5359-0.47940.9974-0.7217-0.83310.06271.11520.2893-0.66050.6747-0.06560.6338-26.515740.793-7.0439
62.3192-1.4271-0.59263.85371.87813.53970.11670.2394-0.1041-0.73130.0278-0.3177-0.09980.3504-0.14460.48-0.08730.14570.2836-0.03040.128913.339110.5739-8.5627
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 381
2X-RAY DIFFRACTION2B10 - 381
3X-RAY DIFFRACTION3C10 - 381
4X-RAY DIFFRACTION4D10 - 381
5X-RAY DIFFRACTION5E10 - 381
6X-RAY DIFFRACTION6F10 - 381

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