[English] 日本語
Yorodumi
- PDB-5nrn: Mtb TMK crystal structure in complex with compound 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nrn
TitleMtb TMK crystal structure in complex with compound 3
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Thymidylate kinase / Nucleotide Binding / inhibitor
Function / homology
Function and homology information


TMP metabolic process / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding ...TMP metabolic process / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / cytoplasm / cytosol
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-95W / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMerceron, R. / Song, L. / Munier-Lehmann, H. / Van Calenbergh, S. / Savvides, S.
CitationJournal: To Be Published
Title: Mtb TMK crystal structure in complex with compound LS3080
Authors: Merceron, R. / Song, L. / Munier-Lehmann, H. / Van Calenbergh, S. / Savvides, S.
History
DepositionApr 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymidylate kinase
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,35811
Polymers45,3252
Non-polymers1,0339
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-70 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.230, 130.230, 120.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21B-434-

HOH

-
Components

#1: Protein Thymidylate kinase / Thymidine monophosphate kinase / dTMP kinase / TMPK


Mass: 22662.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: tmk, Rv3247c / Production host: Escherichia coli (E. coli) / Variant (production host): BLi5 / References: UniProt: P9WKE1, dTMP kinase
#2: Chemical ChemComp-95W / 5-methyl-1-[1-[(6-phenoxypyridin-2-yl)methyl]piperidin-4-yl]pyrimidine-2,4-dione


Mass: 392.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24N4O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 4.3 M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 52835 / % possible obs: 99.8 % / Redundancy: 6.55 % / Biso Wilson estimate: 52.7 Å2 / CC1/2: 1 / Rrim(I) all: 0.057 / Rsym value: 0.053 / Net I/σ(I): 24.45
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.66 % / Mean I/σ(I) obs: 1.69 / Num. unique obs: 3792 / CC1/2: 0.76 / Rrim(I) all: 1.399 / Rsym value: 1.29 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UNR

4unr


Resolution: 2.2→46.043 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.14
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 2640 5 %Random selection
Rwork0.1721 ---
obs0.1735 52822 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 65 280 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063077
X-RAY DIFFRACTIONf_angle_d0.744189
X-RAY DIFFRACTIONf_dihedral_angle_d19.7041829
X-RAY DIFFRACTIONf_chiral_restr0.045462
X-RAY DIFFRACTIONf_plane_restr0.005595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.24010.29321350.27312563X-RAY DIFFRACTION98
2.2401-2.28320.26221370.24922608X-RAY DIFFRACTION100
2.2832-2.32980.2661360.23272611X-RAY DIFFRACTION100
2.3298-2.38050.25981360.21582579X-RAY DIFFRACTION100
2.3805-2.43580.24241370.20792605X-RAY DIFFRACTION100
2.4358-2.49680.23141390.20122630X-RAY DIFFRACTION100
2.4968-2.56430.28251370.2112603X-RAY DIFFRACTION100
2.5643-2.63970.24731370.21322608X-RAY DIFFRACTION100
2.6397-2.72490.2781380.21512640X-RAY DIFFRACTION100
2.7249-2.82230.23971370.22122605X-RAY DIFFRACTION100
2.8223-2.93530.2331380.21222624X-RAY DIFFRACTION100
2.9353-3.06880.20941400.19192649X-RAY DIFFRACTION100
3.0688-3.23060.2081390.18472639X-RAY DIFFRACTION100
3.2306-3.43290.1751390.15322658X-RAY DIFFRACTION100
3.4329-3.69790.16931400.14172643X-RAY DIFFRACTION100
3.6979-4.06980.16841400.13482662X-RAY DIFFRACTION100
4.0698-4.65820.14231420.1252694X-RAY DIFFRACTION100
4.6582-5.8670.17331420.15682709X-RAY DIFFRACTION100
5.867-46.05330.21731510.1852852X-RAY DIFFRACTION99
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)
13.8878-0.7650.94623.35970.48552.02080.04710.35-0.0252-0.2452-0.17320.3516-0.1023-0.15370.12380.3154-0.0201-0.02060.4334-0.0580.3502-44.636-26.4421-18.3207
23.25-0.24340.62811.63950.3531.87970.09430.1708-0.042-0.0259-0.0614-0.08230.11350.2169-0.03580.3269-0.02340.06850.4324-0.03330.351-11.2135-36.2755-5.334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 211)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 211)

+
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