[English] 日本語
Yorodumi
- PDB-1bjg: D221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR IMIDAZ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bjg
TitleD221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR IMIDAZOLIDINE RING
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / ACTIVE SITE MUTANT / REACTION INTERMEDIATE 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
5,10-METHYLENE-6-HYDROFOLIC ACID / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSage, C.R. / Michelitsch, M.D. / Finer-Moore, J. / Stroud, R.M.
Citation
Journal: Biochemistry / Year: 1998
Title: D221 in thymidylate synthase controls conformation change, and thereby opening of the imidazolidine.
Authors: Sage, C.R. / Michelitsch, M.D. / Stout, T.J. / Biermann, D. / Nissen, R. / Finer-Moore, J. / Stroud, R.M.
#1: Journal: Faseb J. / Year: 1993
Title: Stereochemistry of a Multistep/Bipartite Methyl Transfer Reaction: Thymidylate Synthase
Authors: Stroud, R.M. / Finer-Moore, J.S.
#2: Journal: Biochemistry / Year: 1990
Title: Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding Dump and an Anti-Folate
Authors: Montfort, W.R. / Perry, K.M. / Fauman, E.B. / Finer-Moore, J.S. / Maley, G.F. / Hardy, L. / Maley, F. / Stroud, R.M.
#3: Journal: Biochemistry / Year: 1990
Title: Erratum. Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding Dump and an Anti-Folate
Authors: Montfort, W.R. / Perry, K.M. / Fauman, E.B. / Finer-Moore, J.S. / Maley, G.F. / Hardy, L. / Maley, F. / Stroud, R.M.
History
DepositionJun 25, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3403
Polymers30,5591
Non-polymers7822
Water1,65792
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6816
Polymers61,1172
Non-polymers1,5634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556-x+1/2,y,-z+11
Buried area7600 Å2
ΔGint-17 kcal/mol
Surface area19670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.000, 133.000, 133.000
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-296-

HOH

21A-337-

HOH

-
Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 30558.678 Da / Num. of mol.: 1 / Mutation: D169N / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cell line: X2913 / Plasmid: PTHYA-D169N / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-UFP / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 326.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12FN2O8P
#3: Chemical ChemComp-TMF / 5,10-METHYLENE-6-HYDROFOLIC ACID


Mass: 455.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N7O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.21 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.7 / Details: pH 7.7
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 7.8 / PH range high: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 mMpotassium phosphate1drop
32.3 Mammonium sulfate1drop
4100 mM1dropMgCl2
520 mMFdUMP1drop
610 mMCH2H4folate1drop

-
Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 16757 / % possible obs: 94.9 % / Redundancy: 4 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.25 / % possible all: 90.1
Reflection
*PLUS
Num. measured all: 68196
Reflection shell
*PLUS
% possible obs: 90.1 %

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE E. COLI TS

Resolution: 2.3→7 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1514 10 %RANDOM
Rwork0.19 ---
obs0.19 15110 82.1 %-
Displacement parametersBiso mean: 26.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 54 92 2299
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.171.5
X-RAY DIFFRACTIONx_mcangle_it4.532
X-RAY DIFFRACTIONx_scbond_it4.371.5
X-RAY DIFFRACTIONx_scangle_it6.362
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 249 11.2 %
Rwork0.242 1982 -
obs--75.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19CSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3PARAMED.LIGTOPO.FDUMP
X-RAY DIFFRACTION4PARAM_F.LIGTOPO_CLOSED.THF
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

+
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