[English] 日本語
Yorodumi
- PDB-2qk8: Crystal structure of the anthrax drug target, Bacillus anthracis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qk8
TitleCrystal structure of the anthrax drug target, Bacillus anthracis dihydrofolate reductase
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Methotrexate / Pteridine binding / Nucleotide phosphate binding / Pseudo-Rossman fold
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 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
METHOTREXATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBennett, B.C. / Xu, H. / Simmerman, R.F. / Lee, R.E. / Dealwis, C.G.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Crystal structure of the anthrax drug target, Bacillus anthracis dihydrofolate reductase.
Authors: Bennett, B.C. / Xu, H. / Simmerman, R.F. / Lee, R.E. / Dealwis, C.G.
History
DepositionJul 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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)19,6032
Polymers19,1491
Non-polymers4541
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.697, 41.236, 67.032
Angle α, β, γ (deg.)90.00, 119.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-224-

HOH

31A-230-

HOH

DetailsOnly one molecule in the asymmetric unit. Enzyme is functional as a monomer.

-
Components

#1: Protein Dihydrofolate reductase


Mass: 19148.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: Sterne / Gene: dfrA / Plasmid: Champion pET-SUMO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81R22, dihydrofolate reductase
#2: Chemical ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 0.2 M CaCl2, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2006
Details: Bent conical Si-mirror (Rh coated) Bent Ge(111) monochromator
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→58.4 Å / Num. all: 16860 / Num. obs: 10104 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.099 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.342 / % possible all: 76.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0007refinement
BioCARSspecific programdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 1ZDR (Bacillus stearothermophilus DHFR)

1zdr


Resolution: 2.4→22 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.98 / SU ML: 0.263 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2.8 / ESU R: 0.595 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27382 374 5 %RANDOM
Rwork0.24273 ---
obs0.24422 7171 95.68 %-
all-7545 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.402 Å2
Refinement stepCycle: LAST / Resolution: 2.4→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 33 48 1428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221419
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.961920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.675161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16224.24773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.54315242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.184157
X-RAY DIFFRACTIONr_chiral_restr0.1230.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021101
X-RAY DIFFRACTIONr_nbd_refined0.2810.2650
X-RAY DIFFRACTIONr_nbtor_refined0.3350.2901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.27
X-RAY DIFFRACTIONr_mcbond_it0.9591.5842
X-RAY DIFFRACTIONr_mcangle_it1.72521322
X-RAY DIFFRACTIONr_scbond_it2.1673688
X-RAY DIFFRACTIONr_scangle_it3.1554.5598
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 37 -
Rwork0.366 474 -
obs-474 89.96 %

+
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