[English] 日本語
Yorodumi
- PDB-5by6: Crystal structure of Trichinella spiralis thymidylate synthase co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5by6
TitleCrystal structure of Trichinella spiralis thymidylate synthase complexed with dUMP
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Trichinella spiralis / parasitic nematode / protein-ligand complex / methyltransferase
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesTrichinella spiralis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsDowiercial, A. / Jarmula, A. / Rypniewski, W. / Fraczyk, T. / Wilk, P. / Rode, W.
CitationJournal: J. Mol. Graph. Model. / Year: 2017
Title: Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in ...Title: Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS.
Authors: Jarmula, A. / Wilk, P. / Maj, P. / Ludwiczak, J. / Dowiercial, A. / Banaszak, K. / Rypniewski, W. / Ciesla, J. / Dabrowska, M. / Fraczyk, T. / Bronowska, A.K. / Jakowiecki, J. / Filipek, S. / Rode, W.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: PDBE
SupersessionJun 17, 2015ID: 4G9U
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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
B: Thymidylate synthase
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,30117
Polymers142,1784
Non-polymers2,12413
Water15,529862
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2289
Polymers71,0892
Non-polymers1,1397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0748
Polymers71,0892
Non-polymers9856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.695, 65.914, 96.511
Angle α, β, γ (deg.)85.310, 85.330, 67.120
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A18 - 299
2114B18 - 299
3114C18 - 299
4114D18 - 299
1124A308
2124B308
3124C308
4124D308

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.793465, 0.037198, -0.607477), (0.037924, -0.993169, -0.11035), (-0.607433, -0.110597, 0.786635)0.75335, 0.46334, 0.1704
3given(-0.80159, -0.033228, 0.596951), (0.038297, 0.99355, 0.106729), (-0.596647, 0.108414, -0.795147)59.91692, 22.23715, -41.65974
4given(0.999968, -0.006767, 0.004258), (-0.006761, -0.999976, -0.001391), (0.004268, 0.001362, -0.99999)-21.317369, -15.04196, -70.96286
5given(1), (1), (1)
6given(-0.81238, 0.003429, -0.583118), (0.059042, -0.99436, -0.088103), (-0.580132, -0.106001, 0.807596)1.39857, 0.42013, 0.15892
7given(-0.801053, -0.031813, 0.597748), (0.05123, 0.991279, 0.121411), (-0.596397, 0.127879, -0.792438)59.77079, 22.6917, -40.840111
8given(0.999704, 0.009892, 0.022224), (0.009686, -0.99991, 0.009334), (0.022314, -0.009116, -0.999709)-20.316219, -14.7092, -71.396057

-
Components

#1: Protein
Thymidylate synthase


Mass: 35544.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichinella spiralis (invertebrata) / Gene: ts, Tsp_03568 / Plasmid: pET-28a(+)::ST / Production host: Escherichia coli (E. coli) / Strain (production host): TX61- / References: UniProt: Q9NDD3, thymidylate synthase
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, PEG 4K, Magnesium Chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 89350 / % possible obs: 98 % / Redundancy: 5 % / Rmerge(I) obs: 0.128 / Χ2: 0.973 / Net I/av σ(I): 12.563 / Net I/σ(I): 6.1 / Num. measured all: 446073
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.934.90.64444180.88896.5
1.93-1.974.90.51644170.82397.5
1.97-2.014.90.44644060.79697
2.01-2.0550.37944520.82597.2
2.05-2.0950.3544070.82797.3
2.09-2.1450.30144940.84397.5
2.14-2.1950.28544210.88497.4
2.19-2.255.10.26144310.93497.7
2.25-2.325.10.22544541.0198
2.32-2.395.10.21344341.0497.8
2.39-2.4850.19644631.08997.9
2.48-2.585.10.17945221.22498.2
2.58-2.6950.1644761.06698.3
2.69-2.8450.14344961.14998.5
2.84-3.0150.13244861.20698.6
3.01-3.2550.11844811.02198.9
3.25-3.5750.1144951.10298.9
3.57-4.0850.09945380.92599
4.08-5.134.90.08545430.80899.3
5.13-204.90.07145160.97299.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.44 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.96 Å
Translation2.5 Å19.96 Å

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EZ8

4ez8


Resolution: 1.9→19.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2158 / WRfactor Rwork: 0.1611 / FOM work R set: 0.8336 / SU B: 7.908 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1601 / SU Rfree: 0.1516 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 4466 5 %RANDOM
Rwork0.1646 ---
obs0.1674 84834 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.35 Å2 / Biso mean: 31.805 Å2 / Biso min: 12.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.07 Å2-0.55 Å2
2--0.13 Å20.65 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9318 0 136 862 10316
Biso mean--37.95 40.39 -
Num. residues----1140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0199988
X-RAY DIFFRACTIONr_bond_other_d0.0010.029347
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.96413569
X-RAY DIFFRACTIONr_angle_other_deg0.891321558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74551218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53723.547516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.268151733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7731580
X-RAY DIFFRACTIONr_chiral_restr0.1130.21422
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02111317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022471
X-RAY DIFFRACTIONr_mcbond_it1.6091.7654640
X-RAY DIFFRACTIONr_mcbond_other1.6071.7654639
X-RAY DIFFRACTIONr_mcangle_it2.4532.6345814
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A4104MEDIUM POSITIONAL0.50.5
12B4104MEDIUM POSITIONAL0.470.5
13C4104MEDIUM POSITIONAL0.470.5
14D4104MEDIUM POSITIONAL0.450.5
11A4104MEDIUM THERMAL2.432
12B4104MEDIUM THERMAL3.332
13C4104MEDIUM THERMAL2.082
14D4104MEDIUM THERMAL2.92
21A30MEDIUM POSITIONAL0.520.5
22B30MEDIUM POSITIONAL0.540.5
23C30MEDIUM POSITIONAL0.360.5
24D30MEDIUM POSITIONAL0.360.5
21A30MEDIUM THERMAL1.582
22B30MEDIUM THERMAL3.072
23C30MEDIUM THERMAL1.242
24D30MEDIUM THERMAL2.432
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 285 -
Rwork0.242 5667 -
all-5952 -
obs--88.43 %
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)
11.0949-0.0875-0.30880.93690.48070.9942-0.1295-0.1941-0.09210.17630.12520.02110.2470.1510.00430.12880.08280.01370.0680.01570.03277.5167-12.9164-11.903
20.9836-0.3826-0.28211.24660.3921.00840.0022-0.15830.3315-0.06920.0591-0.0714-0.14320.0434-0.06130.05630.0221-0.00520.0453-0.06450.13891.560415.0256-11.9493
31.01260.46790.26881.79340.71281.1358-0.01220.1108-0.2140.13920.0584-0.04480.18260.031-0.04630.0618-0.02180.03230.0279-0.04290.072122.9967-30.0826-58.7476
40.82380.1241-0.00571.28820.67641.1042-0.08570.12780.0499-0.21010.11460.041-0.25630.1451-0.0290.1291-0.07750.01650.0555-0.00090.026129.1159-2.3022-58.8267
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 300
2X-RAY DIFFRACTION2B17 - 304
3X-RAY DIFFRACTION3C18 - 303
4X-RAY DIFFRACTION4D18 - 299

+
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://pdbjlvh1.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