[English] 日本語
Yorodumi
- PDB-1ffl: CRYSTAL STRUCTURE OF THE APO-THYMIDYLATE SYNTHASE R166Q MUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ffl
TitleCRYSTAL STRUCTURE OF THE APO-THYMIDYLATE SYNTHASE R166Q MUTANT
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / METHYLTRANSFERASE
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / 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
Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Fourier Difference Maps / Resolution: 2.94 Å
AuthorsSotelo-Mundo, R.R. / Changchien, L. / Maley, F. / Montfort, W.R.
Citation
Journal: J.Biochem.Mol.Toxicol. / Year: 2006
Title: Crystal structures of thymidylate synthase mutant R166Q: Structural basis for the nearly complete loss of catalytic activity.
Authors: Sotelo-Mundo, R.R. / Changchien, L. / Maley, F. / Montfort, W.R.
#1: Journal: Thesis / Year: 1999
Title: Crystallographic Studies of Thymidylate Synthase : Structure of a Mammalian Enzyme and Analyses of Invariant Non-Catalytic Residues in a Bacterial Enzyme.
Authors: Sotelo-Mundo, R.R.
History
DepositionJul 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THYMIDYLATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)30,5311
Polymers30,5311
Non-polymers00
Water18010
1
A: THYMIDYLATE SYNTHASE

A: THYMIDYLATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)61,0612
Polymers61,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area4270 Å2
ΔGint-20 kcal/mol
Surface area21200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.500, 132.500, 132.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-300-

HOH

DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner.

-
Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 30530.600 Da / Num. of mol.: 1 / Mutation: R166Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: BLUESCRIPT PLASMID SK+ / Production host: Escherichia coli (E. coli)
Strain (production host): XAC 25: LACKS HOST THYMIDYLATE SYNTHASE GENE
References: UniProt: P0A884, thymidylate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: Ammonium sulfate, potassium phosphate, EDTA, DTT, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion / Details: Montfort, W.R., (1990) Biochemistry, 29, 6964.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-9 mg/mLprotein1drop
220 mMpotasssium1drop
32.3 Mammonium1drop
4100 mMdUMP1drop
54.78 mMCB37171drop
620 mMpotassium1reservoir
70.1 mMdisodium ethylenediaminetetraacetic acid1reservoir
820 mMbeta-mercaptoethanol1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 4, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.94→35.335 Å / Num. all: 8138 / Num. obs: 8138 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.4
Reflection shellResolution: 2.94→3.02 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.38 / Num. unique all: 610 / % possible all: 96
Reflection
*PLUS
Lowest resolution: 34 Å / % possible obs: 96 %
Reflection shell
*PLUS
% possible obs: 96 % / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
CNSrefinement
MADNESSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CNSphasing
RefinementMethod to determine structure: Fourier Difference Maps
Starting model: Wildtype Binary Complex of E.coli thymidylate synthase

Resolution: 2.94→33.13 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3374507.52 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0.0001 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 868 10.7 %RANDOM
Rwork0.171 ---
all0.171 8390 --
obs0.171 8138 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.17 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.94→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 0 10 2161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.94→3.12 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 137 10.7 %
Rwork0.258 1147 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CBX.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.7 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.311 / % reflection Rfree: 10.7 % / Rfactor Rwork: 0.258

+
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