[English] 日本語
Yorodumi
- PDB-5chp: T. maritima ThyX in complex with TyC5-03 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5chp
TitleT. maritima ThyX in complex with TyC5-03
ComponentsThymidylate synthase ThyX
KeywordsHYDROLASE / ThyX in complex with inhibitor
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Gyrase A; domain 2 - #170 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-51Q / FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSurade, S. / Luciani, R. / Saxena, P. / Santucci, M. / Ferrari, S. / Venturelli, A. / Marverti, G. / Ponterini, G. / Abell, C.A. / Blundell, T.L. / Costi, M.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
EU FP6 United Kingdom
CitationJournal: To Be Published
Title: Identification of inhibitors targeting substrate-binding site in Mycobacterium tuberculosis FAD-dependent Thymidylate synthase (ThyX) through Virtual Screening: A New study de-fining the ...Title: Identification of inhibitors targeting substrate-binding site in Mycobacterium tuberculosis FAD-dependent Thymidylate synthase (ThyX) through Virtual Screening: A New study de-fining the binding mechanism of Inhibitors
Authors: Surade, S.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 synthase ThyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7813
Polymers27,7781
Non-polymers1,0032
Water4,053225
1
A: Thymidylate synthase ThyX
hetero molecules

A: Thymidylate synthase ThyX
hetero molecules

A: Thymidylate synthase ThyX
hetero molecules

A: Thymidylate synthase ThyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,12312
Polymers111,1124
Non-polymers4,0118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area21480 Å2
ΔGint-70 kcal/mol
Surface area32910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.580, 110.580, 122.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
SymmetryPoint symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral))

-
Components

#1: Protein Thymidylate synthase ThyX / TSase


Mass: 27777.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: thyX, thy1, TM_0449 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WYT0, thymidylate synthase (FAD)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-51Q / (2S)-2-[(3-hydroxy-5-oxo-4,5-dihydro-1,2,4-triazin-6-yl)sulfanyl]propanoic acid / TyC5-03


Mass: 217.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N3O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Hanging drop, soaking regrown crystal with the organic compound
PH range: 6.0-7.5 / Temp details: 16 degrees celcius

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→31.56 Å / Num. obs: 39623 / % possible obs: 99.74 % / Redundancy: 6.2 % / Net I/σ(I): 20

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQ4

1kq4


Resolution: 1.7→30.74 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.371 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 2104 5 %RANDOM
Rwork0.1698 ---
obs0.17131 39622 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 67 225 2109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021953
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5761.992650
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44522.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06215331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0031517
X-RAY DIFFRACTIONr_chiral_restr0.2170.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211478
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 143 -
Rwork0.269 2639 -
obs--97.14 %

+
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