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- PDB-3hv0: Tryptophanyl-tRNA synthetase from Cryptosporidium parvum -

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Basic information

Entry
Database: PDB / ID: 3hv0
TitleTryptophanyl-tRNA synthetase from Cryptosporidium parvum
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / tRNA-ligase / ATP-binding / Aminoacyl-tRNA synthetase / Nucleotide-binding / Protein biosynthesis / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding
Similarity search - Function
Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHAN / Tryptophanyl-tRNA synthetase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.42 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 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 9, 2012Group: Data collection
Revision 1.3Sep 6, 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _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: Tryptophanyl-tRNA synthetase
B: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9664
Polymers90,5582
Non-polymers4082
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.320, 85.220, 73.110
Angle α, β, γ (deg.)90.000, 101.910, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILESERSERAA255 - 45055 - 250
21ILEILESERSERBB255 - 45055 - 250
12GLYGLYLYSLYSAA508 - 587308 - 387
22GLYGLYLYSLYSBB508 - 587308 - 387
13SERSERGLNGLNAA475 - 504275 - 304
23SERSERGLNGLNBB475 - 504275 - 304

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Tryptophanyl-tRNA synthetase


Mass: 45278.758 Da / Num. of mol.: 2 / Fragment: UNP residues 206-593
Source method: isolated from a genetically manipulated source
Details: cleaved
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: cgd7_1490 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5CYP8, tryptophan-tRNA ligase
#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.25 M MgCl2, 0.1 M Bis/Tris pH 6.0, 28% PEG 3350, 10mM ATP, 1mM TCEP, 2mM L-tryptophan, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.42→43.07 Å / Num. obs: 25491 / % possible obs: 95.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 9.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PED ENTRY 3FOC

3foc


Resolution: 2.42→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 1 / SU B: 29.544 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.079 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27286 1277 5 %RANDOM
Rwork0.22693 ---
obs0.22923 24211 94.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.374 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å20 Å21.38 Å2
2---1.27 Å20 Å2
3---4.87 Å2
Refinement stepCycle: LAST / Resolution: 2.42→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5586 0 30 44 5660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225744
X-RAY DIFFRACTIONr_bond_other_d0.0010.023891
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9547761
X-RAY DIFFRACTIONr_angle_other_deg0.89939461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0155698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53924.036275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11515971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2711529
X-RAY DIFFRACTIONr_chiral_restr0.0690.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026383
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021226
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_it0.3171.53514
X-RAY DIFFRACTIONr_mcbond_other0.0741.51418
X-RAY DIFFRACTIONr_mcangle_it0.59825646
X-RAY DIFFRACTIONr_scbond_it1.06532230
X-RAY DIFFRACTIONr_scangle_it1.6994.52115
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11154TIGHT POSITIONAL0.030.05
11520LOOSE POSITIONAL0.045
11154TIGHT THERMAL0.080.5
11520LOOSE THERMAL0.0810
2476TIGHT POSITIONAL0.020.05
2532LOOSE POSITIONAL0.035
2476TIGHT THERMAL0.040.5
2532LOOSE THERMAL0.0510
3178TIGHT POSITIONAL0.020.05
3183LOOSE POSITIONAL0.035
3178TIGHT THERMAL0.050.5
3183LOOSE THERMAL0.0510
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 97 -
Rwork0.313 1666 -
obs--90.27 %
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)
118.4085-2.3995-8.246411.3691-5.723911.3621-1.33850.7724-3.69530.5205-0.4960.1993-0.4668-0.42941.83450.5498-0.12190.17370.5814-0.38560.965520.943-14.067-3.444
23.8689-0.7995-1.60862.49830.85142.74570.01280.1861-0.2387-0.0952-0.06720.1114-0.006-0.05520.05440.1118-0.013-0.03920.1813-0.02950.032418.2672.2987.445
36.9074-3.74960.0936.41220.9361.3811-0.1182-0.6619-0.12480.7360.3408-0.92860.13440.3211-0.22260.3511-0.015-0.1030.5026-0.0460.853245.881-5.2527.121
43.2602-3.21650.90066.0759-0.17771.67340.45240.6956-0.1626-0.8749-0.3144-0.69960.05480.2704-0.1380.3382-0.05240.17060.4576-0.03660.655237.4093.542-2.212
515.30792.4885-5.11520.4087-0.75334.0520.6235-3.57471.61010.0635-0.48910.2936-0.40891.6976-0.13440.51450.0258-0.09211.8977-0.85240.8775-0.82922.94851.523
66.6402-0.6732-1.25042.90611.00222.43120.0197-0.70830.61050.1698-0.08580.11180.0482-0.05150.06610.1132-0.01030.00130.3897-0.13360.08472.64717.7232.356
79.10510.0667-1.71230.2451-0.31141.9807-0.143-1.4711-0.19730.13370.03820.16540.1691-0.05860.10480.3440.0756-0.02570.6512-0.19670.3957-15.18614.4443.9
89.58742.169-2.1720.6411-0.60453.14050.00990.95521.7253-0.03880.30890.1479-0.189-0.383-0.31880.29940.14090.00370.3716-0.04070.7304-10.39128.29727.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A220 - 243
2X-RAY DIFFRACTION2A244 - 453
3X-RAY DIFFRACTION3A454 - 520
4X-RAY DIFFRACTION4A521 - 587
5X-RAY DIFFRACTION5B220 - 250
6X-RAY DIFFRACTION6B251 - 432
7X-RAY DIFFRACTION7B433 - 548
8X-RAY DIFFRACTION8B549 - 587

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