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- PDB-8ssx: Crystal structure of Bacillus anthracis dihydrofolate reductase a... -

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Basic information

Entry
Database: PDB / ID: 8ssx
TitleCrystal structure of Bacillus anthracis dihydrofolate reductase at 1.65-A resolution
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding
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
Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsShaw, G.X. / Li, Y. / Wu, Y. / Yan, H. / Ji, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To be published
Title: Crystal structure of Bacillus anthracis dihydrofolate reductase at 1.65-A resolution
Authors: Shaw, G.X. / Li, Y. / Wu, Y. / Yan, H. / Ji, X.
History
DepositionMay 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,99613
Polymers19,1491
Non-polymers84712
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Bacillus anthracis dihydrofolate reductase
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.623, 59.623, 83.025
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

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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 (anthrax bacterium) / Gene: dfrA, GBAA_2237 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81R22, dihydrofolate reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium sulfate, etc.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2005 / Details: Double crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 21011 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.042 / Χ2: 0.997 / Net I/σ(I): 12.7 / Num. measured all: 144551
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.65-1.7140.43119741.001195.5
1.71-1.786.50.33720541199.7
1.78-1.867.30.22421090.9911100
1.86-1.967.30.13920750.9751100
1.96-2.087.30.09620841.0021100
2.08-2.247.30.06920950.9991100
2.24-2.467.30.051210311100
2.46-2.827.30.04821111.001199.9
2.82-3.557.20.0421531.001199.9
3.55-306.90.01822531.002199.7

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Processing

Software
NameVersionClassification
PHENIXv1.3refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→28.058 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 910 4.34 %Random selection
Rwork0.1841 ---
obs0.1859 20978 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.236 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.8852 Å20 Å2-0 Å2
2---4.8852 Å20 Å2
3----3.8101 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 0 51 200 1599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011603
X-RAY DIFFRACTIONf_angle_d0.9782156
X-RAY DIFFRACTIONf_dihedral_angle_d15.055604
X-RAY DIFFRACTIONf_chiral_restr0.074218
X-RAY DIFFRACTIONf_plane_restr0.004282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6501-1.7370.30081210.2462724X-RAY DIFFRACTION97
1.737-1.84590.24061300.20012852X-RAY DIFFRACTION100
1.8459-1.98830.20251300.18112857X-RAY DIFFRACTION100
1.9883-2.18840.20741290.17522831X-RAY DIFFRACTION100
2.1884-2.50480.19951310.18122879X-RAY DIFFRACTION100
2.5048-3.15520.24481280.18222907X-RAY DIFFRACTION100
3.1552-28.0580.21631410.17363018X-RAY DIFFRACTION100

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