[English] 日本語
Yorodumi
- PDB-7dfr: CRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dfr
TitleCRYSTAL STRUCTURES OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. THE NADP+ HOLOENZYME AND THE FOLATE(DOT)NADP+ TERNARY COMPLEX. SUBSTRATE BINDING AND A MODEL FOR THE TRANSITION STATE
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / OXIDO-REDUCTASE
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / 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
FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBystroff, C. / Oatley, S.J. / Kraut, J.
Citation
Journal: Biochemistry / Year: 1990
Title: Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state.
Authors: Bystroff, C. / Oatley, S.J. / Kraut, J.
#1: Journal: To be Published
Title: Crystal Structure of Unliganded Escherichia Coli Dihydrofolate Reductase. Ligand-Induced Conformational Changes and Cooperativity in Binding
Authors: Bystroff, C. / Kraut, J.
#2: Journal: J.Biol.Chem. / Year: 1982
Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. I. General Features and Binding of Methotrexate
Authors: Bolin, J.T. / Filman, D.J. / Matthews, D.A. / Hamlin, R.C. / Kraut, J.
#3: Journal: Biochemistry / Year: 1987
Title: Effect of Single Amino Acid Replacements on the Folding and Stability of Dihydrofolate Reductase from Escherichia Coli
Authors: Perry, K.M. / Onuffer, J.J. / Touchette, N.A. / Herndon, C.S. / Gittelman, M.S. / Matthews, C.R. / Chen, J.-T. / Mayer, R.J. / Taira, K. / Benkovic, S.J. / Howell, E.E. / Kraut, J.
#4: Journal: J.Biol.Chem. / Year: 1982
Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. II. Environment of Bound Nadph and Implications for Catalysis
Authors: Filman, D.J. / Bolin, J.T. / Matthews, D.A. / Kraut, J.
#5: Journal: J.Biol.Chem. / Year: 1982
Title: Crystal Structure of Avian Dihydrofolate Reductase Containing Phenyltriazine and Nadph
Authors: Volz, K.W. / Matthews, D.A. / Alden, R.A. / Freer, S.T. / Hansch, C. / Kaufman, B.T. / Kraut, J.
#6: Journal: Biochemistry / Year: 1979
Title: Interpretation of Nuclear Magnetic Resonance Spectra for Lactobacillus Casei Dihydrofolate Reductase Based on the X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex
Authors: Matthews, D.A.
#7: Journal: J.Biol.Chem. / Year: 1979
Title: Dihydrofolate Reductase from Lactobacillus Casei. Stereochemistry of Nadph Binding
Authors: Matthews, D.A. / Alden, R.A. / Freer, S.T. / Xuong, N.-H. / Kraut, J.
#8: Journal: J.Biol.Chem. / Year: 1979
Title: Proton Magnetic Resonance Studies on Escherichia Coli Dihydrofolate Reductase. Assignment of Histidine C-2 Protons in Binary Complexes with Folates on the Basis of the Crystal Structure with ...Title: Proton Magnetic Resonance Studies on Escherichia Coli Dihydrofolate Reductase. Assignment of Histidine C-2 Protons in Binary Complexes with Folates on the Basis of the Crystal Structure with Methotrexate and on Chemical Modifications
Authors: Poe, M. / Hoogsteen, K. / Matthews, D.A.
#9: Journal: J.Biol.Chem. / Year: 1978
Title: Dihydrofolate Reductase from Lactobacillus Casei. X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex
Authors: Matthews, D.A. / Alden, R.A. / Bolin, J.T. / Filman, D.J. / Freer, S.T. / Hamlin, R. / Hol, W.G.J. / Kisliuk, R.L. / Pastore, E.J. / Plante, L.T. / Xuong, N.-H. / Kraut, J.
#10: Journal: Biochemistry / Year: 1978
Title: Dihydrofolate Reductase. The Amino Acid Sequence of the Enzyme from a Methotrexate-Resistant Mutant of Escherichia Coli
Authors: Bennett, C.D. / Rodkey, J.A. / Sondey, J.M. / Hirschmann, R.
#11: Journal: Science / Year: 1977
Title: Dihydrofolate Reductase. X-Ray Structure of the Binary Complex with Methotrexate
Authors: Matthews, D.A. / Alden, R.A. / Bolin, J.T. / Freer, S.T. / Hamlin, R. / Xuong, N. / Kraut, J. / Poe, M. / Williams, M. / Hoogsteen, K.
#12: Journal: Biochemistry / Year: 1972
Title: Dihydrofolate Reductase. Purification and Characterization of the Enzyme from an Amethopterin-Resistant Mutant of Escherichia Coli
Authors: Poe, M. / Greenfield, N.J. / Hirshfield, J.M. / Williams, M.N. / Hoogsteen, K.
History
DepositionOct 21, 1988Processing site: BNL
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Structure summary
Category: pdbx_database_status / struct_conf ...pdbx_database_status / struct_conf / struct_conf_type / struct_keywords
Item: _pdbx_database_status.process_site / _struct_keywords.text

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2053
Polymers18,0201
Non-polymers1,1852
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.207, 62.207, 105.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: TEN HYDROPHILIC SIDE CHAINS ARE EITHER ENTIRELY OR PARTIALLY MISSING AND NO COORDINATES ARE INCLUDED FOR THEM IN THIS ENTRY - GLU 17, ARG 44, GLU 48, ARG 52, ARG 98, LYS 106, ASP 116, GLU 120, GLU 129, AND ASP 131.
2: THE PEPTIDE BOND LINKING GLY 95 TO GLY 96 IS IN THE CIS CONFORMATION.
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-402-

HOH

31A-403-

HOH

-
Components

#1: Protein DIHYDROFOLATE REDUCTASE /


Mass: 18020.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-FOL / FOLIC ACID / Folate


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES 16 - 19 FORM A TYPE I BETA TURN. THIS PART OF THE STRUCTURE IS DENOTED AS THE MET 20 LOOP.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/w)PEG60001reservoir
210 mMimidazole hydrochloride1reservior

-
Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. all: 8698 / Num. obs: 8586 / Num. measured all: 68035 / Rmerge F obs: 0.049
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.245 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 80 55 1364
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0340.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.5952
X-RAY DIFFRACTIONp_mcangle_it3.8473
X-RAY DIFFRACTIONp_scbond_it2.6492
X-RAY DIFFRACTIONp_scangle_it3.9663
X-RAY DIFFRACTIONp_plane_restr0.0220.018
X-RAY DIFFRACTIONp_chiral_restr0.2320.18
X-RAY DIFFRACTIONp_singtor_nbd0.2170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2660.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2730.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.45
X-RAY DIFFRACTIONp_staggered_tor23.615
X-RAY DIFFRACTIONp_orthonormal_tor18.215
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Rfactor obs: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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