[English] 日本語
Yorodumi
- PDB-7d6g: Neutron crystal Structure of E.coli Dihydrofolate Reductase compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d6g
TitleNeutron crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+ at pH4.5
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / alpha beta alpha sandwich
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
DEUTERATED WATER / FOLIC ACID / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
Model detailsneutron diffraction
AuthorsWan, Q. / Dealwis, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32071264 China
National Science Foundation (NSF, China)31670790 China
CitationJournal: Acs Catalysis / Year: 2021
Title: Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis
Authors: Wan, Q. / Bennett, B.C. / Wymore, T. / Li, Z. / Wilson, M.A. / Brooks III, C.L. / Langan, P. / Kovalevsky, A. / Dealwis, C.G.
History
DepositionSep 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: 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)19,2594
Polymers18,0191
Non-polymers1,2403
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monodisperse
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint12 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.102, 45.595, 99.113
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Dihydrofolate reductase


Mass: 18019.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: folA, tmrA, b0048, JW0047 / Plasmid: pET-sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY
Nonpolymer detailsFOL in this structure is the tautomer with double bond between N1-C2 atoms instead of N3-C2 atoms. ...FOL in this structure is the tautomer with double bond between N1-C2 atoms instead of N3-C2 atoms. Thus H atom (H31) was observed on N3 atom.

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 40mg/mL DHFR-folate-NADP+ complex, 12% (v/v) PEG 400, 100mM MnCl2, 100mM NaAc, pH4.5

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12911N
22911N
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-00711.54
NUCLEAR REACTOROTHER23.3
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEAug 10, 2014
CUSTOM-MADE2IMAGE PLATEMay 15, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron3CHOPPER
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
23.31
31
Reflection

Entry-ID: 7D6G / Rmerge(I) obs: 0.041 / Diffraction-ID: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Χ2Net I/σ(I)
1.65-401816393.93.90.9624.94
2.1-27.311768191.762.325.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.65-1.753.30.4262.5222300.88177.8
2.1-2.180.3352.35890.9592

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
Refinement

SU ML: 0.11 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 17.25 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 1rx2

1rx2

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.65-27.31X-RAY DIFFRACTION91.126.36688.650.18620.15710.158590416777176815.1191.7611.38
2.1-26.33NEUTRON DIFFRACTION0.21870.17660.178631670184.572.520
Refinement stepCycle: final / Resolution: 1.65→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 129 346 1743
Biso mean--21.63 45.72 -
Num. residues----159
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
2.09-2.630.26471310.20932927NEUTRON DIFFRACTION3058264
2.63-26.330.1951850.15943775NEUTRON DIFFRACTION3960280
1.65-1.750.26781160.21842114X-RAY DIFFRACTION2230671
1.75-1.890.18931580.17322809X-RAY DIFFRACTION2967694
1.89-2.080.21421830.16442877X-RAY DIFFRACTION3060697
2.08-2.380.20241410.15542954X-RAY DIFFRACTION3095697
2.38-30.19721650.16232961X-RAY DIFFRACTION3126697
3-27.310.14421410.13983062X-RAY DIFFRACTION3203695

+
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