[English] 日本語
Yorodumi
- PDB-4yri: Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yri
TitleCrystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 1-(3-bromophenyl)methanamine (Chem 166)
ComponentsHistidyl-tRNA synthetase, putative
KeywordsLigase/Ligase inhibitor / ligase / aminoacyl-tRNA synthetase / aaRS / HisRS / Trypanosoma cruzi / protein-inhibitor complex / Ligase-Ligase inhibitor complex
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Anticodon-binding domain / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-(3-bromophenyl)methanamine / HISTIDINE / histidine--tRNA ligase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKoh, C.-Y. / Hol, W.G.J.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens.
Authors: Koh, C.Y. / Siddaramaiah, L.K. / Ranade, R.M. / Nguyen, J. / Jian, T. / Zhang, Z. / Gillespie, J.R. / Buckner, F.S. / Verlinde, C.L. / Fan, E. / Hol, W.G.
History
DepositionMar 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / pdbx_struct_oper_list
Item: _chem_comp.name / _citation.journal_abbrev ..._chem_comp.name / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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 / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histidyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0309
Polymers51,1861
Non-polymers8458
Water3,585199
1
A: Histidyl-tRNA synthetase, putative
hetero molecules

A: Histidyl-tRNA synthetase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,06118
Polymers102,3712
Non-polymers1,69016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area10510 Å2
ΔGint-94 kcal/mol
Surface area33460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.382, 118.685, 66.108
Angle α, β, γ (deg.)90.000, 92.680, 90.000
Int Tables number5
Space group name H-MI121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Histidyl-tRNA synthetase, putative


Mass: 51185.590 Da / Num. of mol.: 1 / Fragment: UNP residues 45-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053507019.40 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4DA54, histidine-tRNA ligase

-
Non-polymers , 7 types, 207 molecules

#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical ChemComp-4JH / 1-(3-bromophenyl)methanamine


Mass: 186.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8BrN
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 23 % to 28 % PEG 3350, 0.1 M sodium citrate pH 4.8 to 5.3, 1 mM TCEP
PH range: 4.8 to 5.3

-
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: Jan 9, 2013
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→36.94 Å / Num. obs: 31161 / % possible obs: 93.2 % / Redundancy: 2.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.032 / Net I/σ(I): 18.5 / Num. measured all: 87865
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.052.10.3252.6299314440.8590.25958.5
8.94-36.942.90.01577.210003500.9990.01190.3

-
Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
REFMACrefmac_5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LC0

3lc0


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.8 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 1591 5.1 %RANDOM
Rwork0.1903 ---
obs0.1922 29566 93.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.95 Å2 / Biso mean: 35.606 Å2 / Biso min: 13.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å2-0.06 Å2
2--3.44 Å20 Å2
3----1.57 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 63 199 3410
Biso mean--34.52 36.05 -
Num. residues----408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193274
X-RAY DIFFRACTIONr_bond_other_d0.0010.023108
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.9644425
X-RAY DIFFRACTIONr_angle_other_deg0.74637106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5025406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8222.639144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99815525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0251531
X-RAY DIFFRACTIONr_chiral_restr0.0620.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
X-RAY DIFFRACTIONr_mcbond_it0.4051.041635
X-RAY DIFFRACTIONr_mcbond_other0.4051.0411636
X-RAY DIFFRACTIONr_mcangle_it0.7221.5472030
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 56 -
Rwork0.246 1382 -
all-1438 -
obs--58.41 %
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)
12.5472-0.2502-0.14240.76960.10742.5580.02770.23790.38640.00280.0436-0.0039-0.27190.1325-0.07120.1717-0.01230.01180.03570.03460.192469.4621.75923.872
21.0661-0.07590.41436.157-1.11552.25670.07180.63730.3253-0.5445-0.1684-0.1639-0.36450.81410.09660.3875-0.08460.01850.60990.08610.28182.8573.9312.419
32.73120.47480.70451.19780.24053.36670.03440.41320.2104-0.0849-0.0180.0541-0.14270.0772-0.01640.16270.02320.00530.10310.02720.144671.794-1.14413.197
44.7553-0.0215-0.25622.22340.0334.46560.0732-0.0971-0.53-0.12670.0060.23560.4756-0.3462-0.07910.2958-0.1314-0.06090.08220.0810.329740.378-23.23542.684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 212
2X-RAY DIFFRACTION2A213 - 302
3X-RAY DIFFRACTION3A303 - 378
4X-RAY DIFFRACTION4A379 - 478

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more