[English] 日本語
Yorodumi
- PDB-3c0a: Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c0a
TitleLactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative 14C in Multiple Binding Modes-Mode 2
ComponentsThymidylate synthase
KeywordsTRANSFERASE / METHYLTRANSFERASE / STRUCTURE-BASED DRUG DESIGN / Nucleotide biosynthesis
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-14C / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLeone, R. / Mangani, S. / Cancian, L. / Costi, M.P. / Luciani, R. / Ferrari, S.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening
Authors: Mangani, S. / Cancian, L. / Leone, R. / Pozzi, C. / Lazzari, S. / Luciani, R. / Ferrari, S. / Costi, M.P.
History
DepositionJan 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Nov 1, 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_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: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2113
Polymers36,6301
Non-polymers5812
Water1,40578
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4236
Polymers73,2612
Non-polymers1,1624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area5630 Å2
ΔGint-25 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.518, 78.518, 224.377
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Thymidylate synthase / TS / TSase


Mass: 36630.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Plasmid: PKPTSD / Production host: Escherichia coli (E. coli) / Strain (production host): CHI-2913 / References: UniProt: P00469, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-14C / 2-(2-chloropyridin-4-yl)-4-methyl-1H-isoindole-1,3(2H)-dione


Mass: 272.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9ClN2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 4mg/mL LcTS, 1mM EDTA, 40mM dUMP, 20mM TRIS HCl,100mM ammonium phosphate, 5% PEG 400 v/v, 10-12% ligand solution in DMSO, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.008 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.4→50.32 Å / Num. all: 16609 / Num. obs: 16609 / % possible obs: 99 % / Observed criterion σ(I): 1.4 / Redundancy: 10.32 % / Biso Wilson estimate: 55.434 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 5.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 10.69 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 1.4 / Num. unique all: 2363 / Rsym value: 0.528 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCE

1lce


Resolution: 2.4→50.32 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.86 / SU B: 11.16 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(I): 1.4 / ESU R: 0.431 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32615 1505 9.1 %RANDOM
Rwork0.24827 ---
obs0.25541 15087 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.242 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.329 Å0.431 Å
Refinement stepCycle: LAST / Resolution: 2.4→50.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 39 78 2500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212501
X-RAY DIFFRACTIONr_angle_refined_deg2.2011.9613402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8195286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62223.952124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.05515402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7381510
X-RAY DIFFRACTIONr_chiral_restr0.1360.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021931
X-RAY DIFFRACTIONr_nbd_refined0.2530.21135
X-RAY DIFFRACTIONr_nbtor_refined0.320.21592
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.27
X-RAY DIFFRACTIONr_mcbond_it0.9591.51492
X-RAY DIFFRACTIONr_mcangle_it1.67622331
X-RAY DIFFRACTIONr_scbond_it2.17531202
X-RAY DIFFRACTIONr_scangle_it3.2254.51071
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 101 -
Rwork0.294 1100 -
obs-1100 100 %

+
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