[English] 日本語
Yorodumi
- PDB-3m08: Wild Type Dihydrofolate Reductase from Staphylococcus aureus with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m08
TitleWild Type Dihydrofolate Reductase from Staphylococcus aureus with inhibitor RAB1
ComponentsDihydrofolate reductase
KeywordsOxidoreductase/Oxidoreductase inhibitor / folate / dhfr / antimicrobial / antibiotic resistance / NADP / One-carbon metabolism / Oxidoreductase' / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


glycine biosynthetic process / 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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-RAR / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.014 Å
AuthorsBourne, C.R. / Barrow, W.W.
Citation
Journal: Antimicrob.Agents Chemother. / Year: 2010
Title: Inhibition of Antibiotic-Resistant Staphylococcus aureus by the Broad-Spectrum Dihydrofolate Reductase Inhibitor RAB1.
Authors: Bourne, C.R. / Barrow, E.W. / Bunce, R.A. / Bourne, P.C. / Berlin, K.D. / Barrow, W.W.
#1: Journal: Antimicrob.agents chemother. / Year: 2009
Title: Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity
Authors: Bourne, C.R. / Bunce, R.A. / Bourne, P.C. / Berlin, K.D. / Barrow, E.W. / Barrow, W.W.
History
DepositionMar 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7624
Polymers18,4401
Non-polymers1,3223
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.180, 79.180, 107.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Dihydrofolate reductase / / DHFR


Mass: 18440.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Plasmid: pET101d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A017, dihydrofolate reductase
#2: Chemical ChemComp-RAR / 5-(3,4-dimethoxy-5-{(1E)-3-oxo-3-[(1S)-1-propylphthalazin-2(1H)-yl]prop-1-en-1-yl}benzyl)pyrimidine-2,4-diamine / (S)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-propylphthalazin-2(1H)-yl)prop-2-en-1-one


Mass: 486.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30N6O3
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 298 K / Method: sitting drop / pH: 6.5
Details: 15% PEG 6000, 0.15 M sodium acetate, 0.1M MES buffer, pH 6.5, sitting drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.014→42.398 Å / Num. all: 13728 / Num. obs: 13728 / % possible obs: 99.5 % / Redundancy: 5.1 % / Rsym value: 0.037 / Net I/σ(I): 23.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.014-2.125.10.1185.8979319180.11898.7
2.12-2.255.20.0887.7958518400.08898.9
2.25-2.415.20.0699.8903317370.06999.3
2.41-2.65.20.0619.8836716140.06199.6
2.6-2.855.20.05310.6792515320.05399.8
2.85-3.185.20.03814.4718213910.038100
3.18-3.685.10.02719626912310.027100
3.68-4.550.02224.1539810730.022100
4.5-6.374.90.02122.342158630.021100
6.37-42.44.30.02213.222535290.02299.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASER2.1.1phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.014→31.849 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.21 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 1366 10.06 %
Rwork0.175 --
obs0.179 13579 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.685 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 57.3 Å2 / Biso mean: 19.978 Å2 / Biso min: 4.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.782 Å20 Å20 Å2
2---0.782 Å2-0 Å2
3---1.563 Å2
Refinement stepCycle: LAST / Resolution: 2.014→31.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 90 171 1551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051443
X-RAY DIFFRACTIONf_angle_d1.0341972
X-RAY DIFFRACTIONf_chiral_restr0.081218
X-RAY DIFFRACTIONf_plane_restr0.007240
X-RAY DIFFRACTIONf_dihedral_angle_d28.591592
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.014-2.0860.2911320.1891163129596
2.086-2.170.1911290.1661152128197
2.17-2.2680.2251330.1591194132797
2.268-2.3880.2231320.1661181131398
2.388-2.5370.2111350.1651199133498
2.537-2.7330.1971360.1781224136099
2.733-3.0080.2261360.1761221135799
3.008-3.4430.2071390.17312531392100
3.443-4.3360.1861420.15512681410100
4.336-31.8530.2031520.1791358151099
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)
10.52140.1513-0.01370.07040.01750.90810.0159-0.00620.11320.05760.01210.1276-0.26650.0113-0.05320.1381-0.00670.0580.0423-0.00620.1017-4.22330.7603-5.2561
20.79740.2745-0.13770.2204-0.07430.48940.1755-0.26460.29910.2792-0.1118-0.0773-0.25070.1558-0.08160.245-0.0780.02610.0743-0.03270.13796.623736.37795.171
30.65580.1083-0.2250.425-0.19750.53730.0011-0.0401-0.06670.01390.0432-0.0821-0.11690.0096-0.02020.06660.00140.02250.02320.00860.0509-3.903219.0472-3.6097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:56)A1 - 56
2X-RAY DIFFRACTION2(chain A and resid 57:89)A57 - 89
3X-RAY DIFFRACTION3(chain A and resid 90:161)A90 - 161

+
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