[English] 日本語
Yorodumi
- PDB-6e4e: Crystal structure of dihydrofolate reductase from Staphylococcus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e4e
TitleCrystal structure of dihydrofolate reductase from Staphylococcus aureus MW2 bound to NADP and p218
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/Inhibitor / NIAID / DHFR / folate / folic acid / MMV / inhibitor / malaria / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
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-MMV / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of dihydrofolate reductase from Staphylococcus aureus MW2 bound to NADP and p218
Authors: Edwards, T.E. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8403
Polymers20,7371
Non-polymers1,1042
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-3 kcal/mol
Surface area7910 Å2
Unit cell
Length a, b, c (Å)79.000, 79.000, 108.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 20736.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A017, dihydrofolate reductase
#2: 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
#3: Chemical ChemComp-MMV / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid


Mass: 360.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: StauA.01062.a.M1.PS02450 at 17.2 mg/mL with 2 mM NADP and 2 mM p218 against Morpheus screen condition A1 10% PEG 10,000, 20% PEG MME 550, 30 mM CaCl2, 30 mM MgCl2, 0.1 M MES-imidazole pH 6. ...Details: StauA.01062.a.M1.PS02450 at 17.2 mg/mL with 2 mM NADP and 2 mM p218 against Morpheus screen condition A1 10% PEG 10,000, 20% PEG MME 550, 30 mM CaCl2, 30 mM MgCl2, 0.1 M MES-imidazole pH 6.5, crystal tracking ID 299715a1, unique puck ID wan7-6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→42.611 Å / Num. obs: 16429 / % possible obs: 100 % / Redundancy: 14.158 % / Biso Wilson estimate: 31.892 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.134 / Χ2: 0.939 / Net I/σ(I): 14.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.9514.480.5095.2811740.9610.528100
1.95-214.4860.4366.1711440.9660.452100
2-2.0614.4440.3577.3611310.9760.37100
2.06-2.1214.4480.2998.5610920.9830.31100
2.12-2.1914.410.24110.3910660.9870.25100
2.19-2.2714.4370.21411.5310340.9910.221100
2.27-2.3614.3630.19612.49930.990.203100
2.36-2.4514.4280.18813.279630.9880.195100
2.45-2.5614.3450.16214.879180.990.168100
2.56-2.6914.290.14516.498910.9920.15100
2.69-2.8314.2060.13617.018480.9930.141100
2.83-314.2240.12119.368020.9940.125100
3-3.2114.1060.11520.737630.9950.119100
3.21-3.4713.9930.10822.527150.9950.112100
3.47-3.813.9050.10723.276640.9950.111100
3.8-4.2513.850.10623.786010.9920.111100
4.25-4.9113.3810.10523.995490.990.109100
4.91-6.0113.270.10523.844670.9940.109100
6.01-8.512.4840.10822.923760.9910.112100
8.5-42.61110.7180.11122.152380.9810.11798.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FGG

4fgg


Resolution: 1.9→42.611 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.02
RfactorNum. reflection% reflection
Rfree0.2236 800 4.87 %
Rwork0.1802 --
obs0.1824 16426 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.06 Å2 / Biso mean: 38.5604 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 1.9→42.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 0 74 117 1444
Biso mean--33.49 42.56 -
Num. residues----159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9002-2.01920.27221050.218825522657
2.0192-2.17510.26361360.202525352671
2.1751-2.3940.25131210.194525802701
2.394-2.74030.25951560.204425602716
2.7403-3.45230.24151300.188526212751
3.4523-42.6220.18431520.153227782930
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.05260.67980.83961.25730.91381.15560.3632-0.32890.43740.4275-0.07590.3556-0.5899-0.1437-0.05740.5022-0.07080.26210.197-0.10630.3468-4.059329.1754-5.2113
21.52950.245-0.05841.75550.2461.01160.4678-0.57810.57920.8295-0.49360.248-0.3306-0.0922-0.02670.7878-0.33010.18310.4028-0.20150.47275.051437.01244.5552
33.07281.0523-1.09712.2669-0.03294.41050.3441-0.4043-0.0030.21910.0096-0.0739-0.3640.1929-0.28680.2617-0.07480.08920.1501-0.02670.2069-4.01519.9505-4.2361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 50 )A0 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 88 )A51 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 158 )A89 - 158

+
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