[English] 日本語
Yorodumi
- PDB-3lmu: Crystal structure of DTD from Plasmodium falciparum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lmu
TitleCrystal structure of DTD from Plasmodium falciparum
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / IODIDE / DEACYLASE
Function / homology
Function and homology information


Gly-tRNA(Ala) hydrolase 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
IODIDE ION / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SAD / Resolution: 3.3 Å
AuthorsManickam, Y. / Bhatt, T.K. / Khan, S. / Sharma, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of D-tyrosyl-tRNATyr deacylase using home-source Cu Kalpha and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme states
Authors: Yogavel, M. / Khan, S. / Bhatt, T.K. / Sharma, A.
History
DepositionFeb 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 16, 2020Group: Derived calculations / Structure summary / Category: struct / struct_site
Item: _struct.title / _struct_site.pdbx_auth_asym_id ..._struct.title / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
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

-
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
G: D-tyrosyl-tRNA(Tyr) deacylase
H: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,16434
Polymers153,8658
Non-polymers3,30026
Water0
1
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2288
Polymers38,4662
Non-polymers7616
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-10 kcal/mol
Surface area13130 Å2
MethodPISA
2
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,73512
Polymers38,4662
Non-polymers1,26910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-8 kcal/mol
Surface area12200 Å2
MethodPISA
3
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1017
Polymers38,4662
Non-polymers6355
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-10 kcal/mol
Surface area11790 Å2
MethodPISA
4
G: D-tyrosyl-tRNA(Tyr) deacylase
H: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1017
Polymers38,4662
Non-polymers6355
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-13 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.18, 77.18, 214.52
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYchain A and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )AA1 - 101 - 10
12ILEILEILEILEchain A and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )AA30 - 5530 - 55
13TYRTYRTHRTHRchain A and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )AA81 - 9081 - 90
14GLUGLUILEILEchain A and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )AA111 - 155111 - 155
21METMETGLYGLYchain B and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )BB1 - 101 - 10
22ILEILEILEILEchain B and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )BB30 - 5530 - 55
23TYRTYRTHRTHRchain B and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )BB81 - 9081 - 90
24GLUGLUILEILEchain B and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )BB111 - 155111 - 155
31METMETGLYGLYchain C and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )CC1 - 101 - 10
32ILEILEILEILEchain C and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )CC30 - 5530 - 55
33TYRTYRTHRTHRchain C and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )CC81 - 9081 - 90
34GLUGLUILEILEchain C and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )CC111 - 155111 - 155
41METMETGLYGLYchain D and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )DD1 - 101 - 10
42ILEILEILEILEchain D and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )DD30 - 5530 - 55
43TYRTYRTHRTHRchain D and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )DD81 - 9081 - 90
44GLUGLUILEILEchain D and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )DD111 - 155111 - 155
51METMETGLYGLYchain E and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )EE1 - 101 - 10
52ILEILEILEILEchain E and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )EE30 - 5530 - 55
53TYRTYRTHRTHRchain E and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )EE81 - 9081 - 90
54GLUGLUILEILEchain E and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )EE111 - 155111 - 155
61METMETGLYGLYchain F and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )FF1 - 101 - 10
62ILEILEILEILEchain F and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )FF30 - 5530 - 55
63TYRTYRTHRTHRchain F and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )FF81 - 9081 - 90
64GLUGLUILEILEchain F and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )FF111 - 155111 - 155

NCS oper:
IDCodeMatrixVector
1given(-0.091624, -0.2883, 0.953147), (-0.304625, -0.903171, -0.302466), (0.948055, -0.318065, -0.005071)-28.819401, 58.2952, 45.6642
2given(-0.232799, 0.299865, 0.925141), (0.668606, -0.641459, 0.376161), (0.706237, 0.706124, -0.05116)-72.474197, 47.439701, -20.804199
3given(0.494037, 0.831534, -0.253927), (-0.756603, 0.267289, -0.596748), (-0.428345, 0.486938, 0.761191)-55.405602, 43.757702, -38.1819
4given(0.63094, 0.685332, -0.363641), (-0.698506, 0.297807, -0.650692), (-0.337646, 0.664553, 0.666607)-50.8246, 7.62969, -76.205803
5given(-0.162204, 0.491217, 0.855801), (0.554587, -0.671965, 0.490812), (0.816163, 0.554228, -0.163427)-98.685799, 90.058098, -4.38311

-
Components

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


Mass: 19233.084 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: DTD, PF11_0095 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q8IIS0, Hydrolases; Acting on ester bonds
#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: I

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.76 % / Mosaicity: 0.583 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG1500, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 29, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 18914 / % possible obs: 100 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.162 / Χ2: 1.328 / Net I/σ(I): 6.8
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.516 / Num. unique all: 1869 / Χ2: 1.125 / % possible all: 100

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.3→33.958 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.36 / σ(F): 1.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 971 5.15 %
Rwork0.185 --
obs0.189 18839 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.34 Å2 / ksol: 0.287 e/Å3
Displacement parametersBiso max: 118.19 Å2 / Biso mean: 48.635 Å2 / Biso min: 18.57 Å2
Baniso -1Baniso -2Baniso -3
1--7.12 Å2-0 Å20 Å2
2---7.12 Å20 Å2
3---14.241 Å2
Refinement stepCycle: LAST / Resolution: 3.3→33.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9253 0 26 0 9279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099441
X-RAY DIFFRACTIONf_angle_d1.15412835
X-RAY DIFFRACTIONf_chiral_restr0.071487
X-RAY DIFFRACTIONf_plane_restr0.0031636
X-RAY DIFFRACTIONf_dihedral_angle_d20.2133242
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A720X-RAY DIFFRACTIONPOSITIONAL0.048
12B720X-RAY DIFFRACTIONPOSITIONAL0.048
13C719X-RAY DIFFRACTIONPOSITIONAL0.045
14D716X-RAY DIFFRACTIONPOSITIONAL0.048
15E718X-RAY DIFFRACTIONPOSITIONAL0.05
16F717X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.298-3.4710.2881440.21425342678100
3.471-3.6890.2781420.19725642706100
3.689-3.9730.2771440.18825142658100
3.973-4.3720.221250.15525952720100
4.372-5.0030.2011390.14825412680100
5.003-6.2970.2591280.18325632691100
6.297-33.960.2661490.1982557270699

+
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