[English] 日本語
Yorodumi
- PDB-3d84: Structural Analysis of a Holo Enzyme Complex of Mouse Dihydrofola... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d84
TitleStructural Analysis of a Holo Enzyme Complex of Mouse Dihydrofolate Reductase with NADPH and a Ternary Complex with the Potent and Selective Inhibitor 2.4-Diamino-6-(-2'-hydroxydibenz[b,f]azepin-5-yl)methylpteridine
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / mouse DHFR holo enzyme and ternary ligand complex / NADP / One-carbon metabolism
Function / homology
Function and homology information


Metabolism of folate and pterines / regulation of removal of superoxide radicals / dihydrofolic acid binding / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / response to methotrexate / tetrahydrofolate interconversion / axon regeneration / dihydrofolate metabolic process / folic acid metabolic process ...Metabolism of folate and pterines / regulation of removal of superoxide radicals / dihydrofolic acid binding / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / response to methotrexate / tetrahydrofolate interconversion / axon regeneration / dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / positive regulation of nitric-oxide synthase activity / response to nicotine / NADP binding / mRNA binding / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCody, V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structural analysis of a holoenzyme complex of mouse dihydrofolate reductase with NADPH and a ternary complex with the potent and selective inhibitor 2,4-diamino-6-(2'-hydroxydibenz[b,f]azepin- ...Title: Structural analysis of a holoenzyme complex of mouse dihydrofolate reductase with NADPH and a ternary complex with the potent and selective inhibitor 2,4-diamino-6-(2'-hydroxydibenz[b,f]azepin-5-yl)methylpteridine.
Authors: Cody, V. / Pace, J. / Rosowsky, A.
History
DepositionMay 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4334
Polymers21,5041
Non-polymers9303
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.226, 61.172, 43.150
Angle α, β, γ (deg.)90.00, 118.26, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Dihydrofolate reductase


Mass: 21503.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: jm105 / Gene: Dhfr / Plasmid: pPH70d / Production host: Escherichia coli (E. coli) / References: UniProt: P00375, 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10 mM Hepes, pH 7.4, 17 mM Na acetate, pH 6.5, 85 mM Tris HCl, 25% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2004 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→38.01 Å / Num. all: 14934 / Num. obs: 13551 / % possible obs: 90.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.05 / Net I/σ(I): 0.033
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 14 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 0.9 / Num. unique all: 750 / Rsym value: 0.495 / % possible all: 50.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fzj

2fzj


Resolution: 1.9→23.83 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.432 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.193 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 684 5 %RANDOM
Rwork0.18684 ---
all0.21 13551 --
obs0.18902 12865 90.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refine analyzeLuzzati sigma a free: 0.018 Å
Refinement stepCycle: LAST / Resolution: 1.9→23.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 60 83 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221620
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216
X-RAY DIFFRACTIONr_angle_refined_deg2.0632.0282194
X-RAY DIFFRACTIONr_angle_other_deg1.15332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4835187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37424.24773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71915293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9531511
X-RAY DIFFRACTIONr_chiral_restr0.1390.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021203
X-RAY DIFFRACTIONr_nbd_refined0.2180.2694
X-RAY DIFFRACTIONr_nbd_other0.270.221
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21061
X-RAY DIFFRACTIONr_nbtor_other0.1440.23
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.211
X-RAY DIFFRACTIONr_mcbond_it1.0961.5969
X-RAY DIFFRACTIONr_mcangle_it1.81421526
X-RAY DIFFRACTIONr_scbond_it2.7673757
X-RAY DIFFRACTIONr_scangle_it4.114.5668
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 28 -
Rwork0.253 502 -
obs--48.94 %

+
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