[English] 日本語
Yorodumi
- PDB-3hb8: Structures of Thymidylate Synthase R163K with Substrates and Inhi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hb8
TitleStructures of Thymidylate Synthase R163K with Substrates and Inhibitors Show Subunit Asymmetry
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyl transferase / Methyltransferase / Nucleotide biosynthesis
Function / homology
Function and homology information


uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / folic acid binding / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / liver regeneration / response to toxic substance / circadian rhythm / response to ethanol / methylation / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytosol / cytoplasm
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
PHOSPHATE ION / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.74 Å
AuthorsGibson, L.M. / Lovelace, L.L. / Lebioda, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structures of human thymidylate synthase R163K with dUMP, FdUMP and glutathione show asymmetric ligand binding.
Authors: Gibson, L.M. / Celeste, L.R. / Lovelace, L.L. / Lebioda, L.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: 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 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase
C: Thymidylate synthase
D: Thymidylate synthase
E: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,97513
Polymers178,6755
Non-polymers1,3018
Water2,234124
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9976
Polymers71,4702
Non-polymers5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-26 kcal/mol
Surface area22130 Å2
MethodPISA
2
C: Thymidylate synthase
hetero molecules

C: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0864
Polymers71,4702
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5480 Å2
ΔGint-32 kcal/mol
Surface area22580 Å2
MethodPISA
3
D: Thymidylate synthase
E: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9355
Polymers71,4702
Non-polymers4653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-29 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.459, 122.149, 99.157
Angle α, β, γ (deg.)90.000, 114.550, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Thymidylate synthase / TSase / TS


Mass: 35734.926 Da / Num. of mol.: 5 / Mutation: R163K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Production host: Escherichia coli (E. coli) / References: UniProt: P04818, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10-20% PEG 4000, 20mM BME, 3mM potassium phosphate, 0.1M TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 52210 / % possible obs: 96.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.069 / Χ2: 2.897 / Net I/σ(I): 28.126
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.268 / Num. unique all: 4462 / Χ2: 1.201 / % possible all: 82.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementResolution: 2.74→50 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.781 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.261 5079 9.1 %
Rwork0.21 45096 -
obs-50175 89.5 %
Solvent computationBsol: 28.449 Å2
Displacement parametersBiso max: 117.88 Å2 / Biso mean: 59.982 Å2 / Biso min: 14.81 Å2
Baniso -1Baniso -2Baniso -3
1-19.618 Å20 Å28.128 Å2
2---6.882 Å20 Å2
3----12.736 Å2
Refinement stepCycle: LAST / Resolution: 2.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11336 0 82 124 11542
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.262
X-RAY DIFFRACTIONc_mcbond_it1.7052
X-RAY DIFFRACTIONc_scbond_it2.9963
X-RAY DIFFRACTIONc_mcangle_it2.8242.5
X-RAY DIFFRACTIONc_scangle_it4.4053.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.74-2.76
2.76-2.780.42620.27657
2.78-2.80.332530.318559612
2.8-2.820.379740.341776850
2.82-2.840.371970.325812909
2.84-2.860.457880.351873961
2.86-2.880.406940.356856950
2.88-2.90.417880.359883971
2.9-2.930.3831010.325852953
2.93-2.950.361160.31868984
2.95-2.980.3811090.3249041013
2.98-30.3881030.307888991
3-3.030.388960.3299101006
3.03-3.060.321900.2999641054
3.06-3.090.4631000.309899999
3.09-3.120.438960.2999041000
3.12-3.150.3571220.2949311053
3.15-3.180.3231030.39131016
3.18-3.210.3781040.289871091
3.21-3.250.3471030.2739231026
3.25-3.290.323860.279691055
3.29-3.320.3281160.2699661082
3.32-3.360.2951060.2649251031
3.36-3.410.3131100.26710001110
3.41-3.450.3191000.2579151015
3.45-3.50.2811100.2529961106
3.5-3.550.3111030.2319611064
3.55-3.60.3261020.25510111113
3.6-3.660.3191050.2329601065
3.66-3.720.2681060.2239871093
3.72-3.780.2671010.2159491050
3.78-3.850.3221170.23710021119
3.85-3.930.2511090.2179791088
3.93-4.010.251140.1859691083
4.01-4.090.2061170.1749771094
4.09-4.190.239980.1779841082
4.19-4.290.2141380.169601098
4.29-4.410.1771050.13610031108
4.41-4.540.1821190.1399641083
4.54-4.690.1821240.1329821106
4.69-4.850.1881110.1359981109
4.85-5.050.2221160.169951111
5.05-5.280.2011200.1669891109
5.28-5.560.2421250.189781103
5.56-5.90.2661000.20110071107
5.9-6.360.2631200.2079911111
6.36-70.2511280.1989811109
7-8.010.1851090.14610181127
8.01-10.090.1821270.12810041131
10.09-500.010.212980.1979691067
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramHicupCNS_TOPPAR:protein.topHIcup
X-RAY DIFFRACTION2CNS_TOPPAR:trs.paramCNS_TOPPAR:trs.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:dUMP.paramCNS_TOPPAR:dUMP.top

+
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