[English] 日本語
Yorodumi
- PDB-2hqp: Solution structure of L.casei dihydrofolate reductase complexed w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hqp
TitleSolution structure of L.casei dihydrofolate reductase complexed with NADPH, 32 structures
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR
Function / homology
Function and homology information


response to methotrexate / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to antibiotic / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsPolshakov, V.I. / Birdsall, B.
CitationJournal: TO BE PUBLISHED
Title: Structural insights into cooperative effects of ligand binding to L. casei dihydrofolate redutase
Authors: Smurnyy, Y. / Kovalevskaya, N. / Birdsall, B. / Polshakov, V.I. / Feeney, J.
History
DepositionJul 19, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0772
Polymers18,3321
Non-polymers7451
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 32all calculated structures submitted
RepresentativeModel #1minimal rmsd when superimpose all other members of the family

-
Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 18331.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: folA, dhfR / Plasmid: PMT702 / Production host: Escherichia coli (E. coli) / Strain (production host): Nf1 / References: UniProt: P00381, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1222D NOESY
1332D NOESY
142COSY
1522D 15N-rejected NOESY
161IPAP

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM DHFR-15N/NADPH, 50mM phosphate buffer, 5% DMPC/DHPC, 90% H2O, 10% D2O90% H2O/10% D2O
21mM DHFR-15N/NADPH, 50mM phosphate buffer, 100% H2O100% H2O
31mM DHFR-15N/NADPH, 50mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM KCl / pH: 6.5 / Pressure: ambient / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian UNITYVarianUNITY6002
Varian UNITYPLUSVarianUNITYPLUS5003
Bruker AVANCEBrukerAVANCE6004

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Inccollection
NMRPipe1998-2001Delaglioprocessing
Sparky3.8UCSFdata analysis
Xplor-NIH3.11Clorerefinement
CNS1Brungerrefinement
ARIA2.0aNilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Annealing from 1000K down to 0K with 25K step, 10ps of dynamics at each step
NMR representativeSelection criteria: minimal rmsd when superimpose all other members of the family
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 32 / Conformers submitted total number: 32

+
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