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- PDB-9cum: Q67H mutant of R67 DHFR complexed with Congo Red -

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Basic information

Entry
Database: PDB / ID: 9cum
TitleQ67H mutant of R67 DHFR complexed with Congo Red
ComponentsDihydrofolate reductase type 2
KeywordsOXIDOREDUCTASE / Congo Red / inhibitor / complex
Function / homology
Function and homology information


response to methotrexate / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / response to xenobiotic stimulus / response to antibiotic
Similarity search - Function
Dihydrofolate reductase, type II / R67 dihydrofolate reductase / Mechanosensitive ion channel MscS, beta-domain superfamily / Electron transport accessory-like domain superfamily
Similarity search - Domain/homology
Chem-CGO / Dihydrofolate reductase type 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsNarayana, N. / Narendra, A.N.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
Citation
Journal: Sci Rep / Year: 2025
Title: Crystal structure of the plasmid-encoded R67 dihydrofolate reductase complexed with Congo red an amyloid binding dye.
Authors: Narendra, A.N. / Howell, E.E. / Narayana, N.
#1: Journal: Protein Sci / Year: 2007
Title: Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode.
Authors: Divya, N. / Grifith, E. / Narayana, N.
#2: Journal: Nat Struct Biol / Year: 1995
Title: A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site.
Authors: Narayana, N. / Matthews, D.A. / Howell, E.E. / Nguyen-huu, X.
#3: Journal: ACS Omega / Year: 2019
Title: Structure-Based Design of Dimeric Bisbenzimidazole Inhibitors to an Emergent Trimethoprim-Resistant Type II Dihydrofolate Reductase Guides the Design of Monomeric Analogues.
Authors: Toulouse, J.L. / Yachnin, B.J. / Ruediger, E.H. / Deon, D. / Gagnon, M. / Saint-Jacques, K. / Ebert, M.C.C.J.C. / Forge, D. / Bastien, D. / Colin, D.Y. / Vanden Eynde, J.J. / Marinier, A. / ...Authors: Toulouse, J.L. / Yachnin, B.J. / Ruediger, E.H. / Deon, D. / Gagnon, M. / Saint-Jacques, K. / Ebert, M.C.C.J.C. / Forge, D. / Bastien, D. / Colin, D.Y. / Vanden Eynde, J.J. / Marinier, A. / Berghuis, A.M. / Pelletier, J.N.
#4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2006
Title: High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site.
Authors: Narayana, N.
History
DepositionJul 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8176
Polymers6,7431
Non-polymers1,0745
Water2,522140
1
A: Dihydrofolate reductase type 2
hetero molecules

A: Dihydrofolate reductase type 2
hetero molecules

A: Dihydrofolate reductase type 2
hetero molecules

A: Dihydrofolate reductase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,26724
Polymers26,9704
Non-polymers4,29720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Buried area8400 Å2
ΔGint-130 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.303, 67.303, 52.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-148-

HOH

21A-150-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydrofolate reductase type 2 / Dihydrofolate reductase type II


Mass: 6742.546 Da / Num. of mol.: 1 / Mutation: Q67H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00383, dihydrofolate reductase

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Non-polymers , 5 types, 145 molecules

#2: Chemical ChemComp-CGO / sodium 3,3'-(1E,1'E)-biphenyl-4,4'-diylbis(diazene-2,1-diyl)bis(4-aminonaphthalene-1-sulfonate) / congo red


Mass: 696.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H22N6Na2O6S2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: MPD, potassium phosphate, congo red

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.15→15 Å / Num. obs: 21571 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Rsym value: 0.043 / Net I/σ(I): 59.9
Reflection shellResolution: 1.15→1.19 Å / Num. unique obs: 2135 / Rsym value: 0.113 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.627 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.13464 1024 4.7 %RANDOM
Rwork0.12193 ---
obs0.12258 20547 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.157 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.15→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms445 0 42 140 627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.012518
X-RAY DIFFRACTIONr_bond_other_d0.0040.016492
X-RAY DIFFRACTIONr_angle_refined_deg2.4561.823715
X-RAY DIFFRACTIONr_angle_other_deg1.1791.7681099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.036563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.0498.754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9521069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.4330.274
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02128
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2350.841237
X-RAY DIFFRACTIONr_mcbond_other3.363237
X-RAY DIFFRACTIONr_mcangle_it4.7561.5296
X-RAY DIFFRACTIONr_mcangle_other4.7982.151297
X-RAY DIFFRACTIONr_scbond_it5.131.176281
X-RAY DIFFRACTIONr_scbond_other5.132282
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1872.068417
X-RAY DIFFRACTIONr_long_range_B_refined23.04719.64699
X-RAY DIFFRACTIONr_long_range_B_other20.87712.97613
X-RAY DIFFRACTIONr_rigid_bond_restr5.2783518
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.151→1.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.11 66 -
Rwork0.089 1496 -
obs--99.24 %

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