[English] 日本語
Yorodumi
- PDB-3f8z: Human Dihydrofolate Reductase Structural Data with Active Site Mu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f8z
TitleHuman Dihydrofolate Reductase Structural Data with Active Site Mutant Enzyme Complexes
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / active site mutants ligand complex human dihydrofolate reductase / NADP / One-carbon metabolism
Function / homology
Function and homology information


regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / folic acid binding / axon regeneration / dihydrofolate metabolic process / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / folic acid binding / axon regeneration / dihydrofolate metabolic process / G1/S-Specific Transcription / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / one-carbon metabolic process / mRNA regulatory element binding translation repressor activity / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 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-DH1 / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsCody, V. / Pace, J. / Makin, J. / Piraino, J. / Queener, S.F. / Rosowsky, A.
CitationJournal: Biochemistry / Year: 2009
Title: Correlations of Inhibitor Kinetics for Pneumocystis jirovecii and Human Dihydrofolate Reductase with Structural Data for Human Active Site Mutant Enzyme Complexes.
Authors: Cody, V. / Pace, J. / Makin, J. / Piraino, J. / Queener, S.F. / Rosowsky, A.
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 30, 2014Group: Data collection
Revision 1.3Oct 20, 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9858
Polymers21,4131
Non-polymers1,5727
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.416, 84.416, 77.934
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Dihydrofolate reductase


Mass: 21412.646 Da / Num. of mol.: 1 / Mutation: Q35S, N64S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR, DHFRP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P00374, dihydrofolate reductase
#2: Chemical ChemComp-DH1 / 2,4-DIAMINO-5-[2-METHOXY-5-(4-CARBOXYBUTYLOXY)BENZYL]PYRIMIDINE


Mass: 346.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N4O4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 100 mM potassium phosphate, pH 6.9, 60% ammonium sulfate, 3% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 287K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 10, 2008 / 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: 1.68→26.25 Å / Num. obs: 17593 / % possible obs: 74.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 32.56 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.039 / Net I/σ(I): 16.3
Reflection shellResolution: 1.68→1.77 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 1.3 / Num. unique all: 590 / Rsym value: 0.261 / % possible all: 17

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u72

1u72


Resolution: 2.01→26.66 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.743 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / ESU R: 0.199 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21877 705 5.3 %RANDOM
Rwork0.16055 ---
obs0.16351 12666 97.02 %-
all-12666 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.993 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.186 Å
Refinement stepCycle: LAST / Resolution: 2.01→26.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 98 276 1871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221630
X-RAY DIFFRACTIONr_angle_refined_deg1.9692.0512212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3295185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31824.63869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98615285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.625158
X-RAY DIFFRACTIONr_chiral_restr0.1520.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021196
X-RAY DIFFRACTIONr_nbd_refined0.2190.2712
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21050
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3130.232
X-RAY DIFFRACTIONr_mcbond_it1.0731.5974
X-RAY DIFFRACTIONr_mcangle_it1.64521509
X-RAY DIFFRACTIONr_scbond_it2.7113777
X-RAY DIFFRACTIONr_scangle_it3.9114.5703
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 52 -
Rwork0.168 924 -
obs--94.94 %

+
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