[English] 日本語
Yorodumi
- PDB-3ko3: D-tyrosyl-tRNA(Tyr) deacylase from Plasmodium falciparum incomple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ko3
TitleD-tyrosyl-tRNA(Tyr) deacylase from Plasmodium falciparum incomplex with ADP, obtained through soaking native enzyme crystal with the ATP
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / Deacylase / ADP
Function / homology
Function and homology information


Gly-tRNA(Ala) deacylase activity / D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / tRNA binding / nucleotide binding / cytoplasm
Similarity search - Function
D-aminoacyl-tRNA deacylase DTD / D-Tyr-tRNA(Tyr) deacylase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsManickam, Y. / Bhatt, T.K. / Sharma, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Ligand-bound Structures Provide Atomic Snapshots for the Catalytic Mechanism of D-Amino Acid Deacylase
Authors: Bhatt, T.K. / Yogavel, M. / Wydau, S. / Berwal, R. / Sharma, A.
History
DepositionNov 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,8267
Polymers115,3996
Non-polymers4271
Water1,42379
1
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase


Theoretical massNumber of molelcules
Total (without water)38,4662
Polymers38,4662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-8 kcal/mol
Surface area14320 Å2
MethodPISA
2
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8933
Polymers38,4662
Non-polymers4271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-11 kcal/mol
Surface area14340 Å2
MethodPISA
3
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase


Theoretical massNumber of molelcules
Total (without water)38,4662
Polymers38,4662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-9 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.786, 53.241, 91.793
Angle α, β, γ (deg.)72.520, 77.850, 88.920
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
D-tyrosyl-tRNA(Tyr) deacylase


Mass: 19233.084 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: dtd / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q8IIS0, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.04 Å3/Da / Density % sol: 39.79 % / Mosaicity: 1.263 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.1M MES, pH 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 6.2-6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 27620 / % possible obs: 95.9 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.092 / Χ2: 0.821 / Net I/σ(I): 5.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.481 / Num. unique all: 2388 / Χ2: 0.675 / % possible all: 82.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.864 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 17.266 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2215 10 %RANDOM
Rwork0.179 ---
obs0.188 19900 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.51 Å2 / Biso mean: 35.355 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å2-2.15 Å2-1.93 Å2
2---1.11 Å21.75 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7630 0 27 79 7736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227805
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.95310535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9665924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.80625.485392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.257151499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2061531
X-RAY DIFFRACTIONr_chiral_restr0.0930.21173
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025766
X-RAY DIFFRACTIONr_nbd_refined0.2250.23472
X-RAY DIFFRACTIONr_nbtor_refined0.3170.25122
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.26
X-RAY DIFFRACTIONr_mcbond_it0.6211.54688
X-RAY DIFFRACTIONr_mcangle_it1.12227461
X-RAY DIFFRACTIONr_scbond_it1.22633525
X-RAY DIFFRACTIONr_scangle_it2.024.53067
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 162 -
Rwork0.26 1431 -
all-1593 -
obs--95.68 %

+
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