[English] 日本語
Yorodumi
- PDB-1ohj: HUMAN DIHYDROFOLATE REDUCTASE, MONOCLINIC (P21) CRYSTAL FORM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ohj
TitleHUMAN DIHYDROFOLATE REDUCTASE, MONOCLINIC (P21) CRYSTAL FORM
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


G1/S-Specific Transcription / Metabolism of folate and pterines / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / methotrexate binding / response to methotrexate / dihydrofolate metabolic process / sequence-specific mRNA binding ...G1/S-Specific Transcription / Metabolism of folate and pterines / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / methotrexate binding / response to methotrexate / dihydrofolate metabolic process / sequence-specific mRNA binding / axon regeneration / folic acid metabolic process / folic acid binding / dihydrofolate reductase / dihydrofolate reductase activity / regulation of transcription involved in G1/S transition of mitotic cell cycle / translation repressor activity, mRNA regulatory element binding / tetrahydrofolate biosynthetic process / NADPH binding / one-carbon metabolic process / positive regulation of nitric-oxide synthase activity / negative regulation of translation / drug binding / NADP binding / oxidation-reduction process / mRNA binding / mitochondrion / cytosol
Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase-like domain superfamily / Dihydrofolate reductase conserved site / Dihydrofolate reductase domain
Dihydrofolate reductase
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsCody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W.
Citation
Journal: Biochemistry / Year: 1997
Title: Comparison of two independent crystal structures of human dihydrofolate reductase ternary complexes reduced with nicotinamide adenine dinucleotide phosphate and the very tight-binding inhibitor PT523.
Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Rosowsky, A. / Blakley, R.L.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Methotrexate-Resistant Variants of Human Dihydrofolate Reductase with Substitutions of Leucine 22. Kinetics, Crystallography, and Potential as Selectable Markers
Authors: Lewis, W.S. / Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Chunduru, S.K. / Spencer, H.T. / Appleman, J.R. / Blakley, R.L.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: Methotrexate-Resistant Variants of Human Dihydrofolate Reductase. Effects of Phe31 Substitutions
Authors: Chunduru, S.K. / Cody, V. / Luft, J.R. / Pangborn, W. / Appleman, J.R. / Blakley, R.L.
#3: Journal: Anti-Cancer Drug Des. / Year: 1992
Title: Crystal Structure Determination at 2.3 A of Recombinant Human Dihydrofolate Reductase Ternary Complex with Nadph and Methotrexate-Gamma-Tetrazole
Authors: Cody, V. / Luft, J.R. / Ciszak, E. / Kalman, T.I. / Freisheim, J.H.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 17, 1997-
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6693
Polymers21,3501
Non-polymers1,3192
Water18010
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)65.822, 40.350, 75.150
Angle α, β, γ (deg.)90.00, 109.74, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide DIHYDROFOLATE REDUCTASE / / DHFR


Mass: 21349.525 Da / Num. of mol.: 1
Details: COMPLEXED WITH NADPH AND PT523 NA-(4-AMINO-4-DEOXYPTEROYL)-ND-HEMIPHTHALOYL-L-ORNITHINE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POTENTIAL / Production host: Escherichia coli (E. coli) / Strain (production host): JM107 / References: UniProt: P00374, 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-COP / N-(4-CARBOXY-4-{4-[(2,4-DIAMINO-PTERIDIN-6-YLMETHYL)-AMINO]-BENZOYLAMINO}-BUTYL)-PHTHALAMIC ACID / PT523


Mass: 573.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27N9O6
#4: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-ID
140 %PEG4000drop
20.2 Msodium acetatedrop
30.1 MTris-HCldrop
440 %PEG4000reservoir
50.2 Msodium acetatereservoir
60.1 MTris-HClreservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→8 Å / Num. obs: 5276 / % possible obs: 93.4 % / Observed criterion σ(I): 2

-
Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2.5→8 Å
RfactorNum. reflection% reflection
Rwork0.208 --
Obs-5276 93.4 %
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 91 10 1602
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
p_bond_d0.0140.02
p_angle_d0.0520.04
p_angle_deg
p_planar_d0.0450.05
p_hb_or_metal_coord
p_mcbond_it0.691
p_mcangle_it1.2331.5
p_scbond_it0.5781
p_scangle_it1.0181.5
p_plane_restr0.0110.02
p_chiral_restr0.1890.15
p_singtor_nbd0.2370.5
p_multtor_nbd0.3070.5
p_xhyhbond_nbd
p_xyhbond_nbd0.3460.5
p_planar_tor2.13
p_staggered_tor2315
p_orthonormal_tor
p_transverse_tor19.515
p_special_tor010
Refinement
*PLUS
Rfactor obs: 0.208
Displacement parameters
*PLUS
Biso mean: 16.86 Å2

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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