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- PDB-7r6g: Crystal structure of DfrA5 dihydrofolate reductase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7r6g
TitleCrystal structure of DfrA5 dihydrofolate reductase in complex with TRIMETHOPRIM and NADPH
ComponentsDihydrofolate reductase type 5
KeywordsOXIDOREDUCTASE / dihydrofolate reductase
Function / homology
Function and homology information


response to methotrexate / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to antibiotic / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Chem-NDP / TRIMETHOPRIM / Dihydrofolate reductase type 5
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsEstrada, A. / Wright, D. / Krucinska, J. / Erlandsen, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1 R01AI111957 United States
CitationJournal: Commun Biol / Year: 2022
Title: Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens.
Authors: Krucinska, J. / Lombardo, M.N. / Erlandsen, H. / Estrada, A. / Si, D. / Viswanathan, K. / Wright, D.L.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase type 5
B: Dihydrofolate reductase type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2627
Polymers35,0942
Non-polymers2,1685
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-33 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.530, 99.530, 42.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 157 / Label seq-ID: 1 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Dihydrofolate reductase type 5 / Dihydrofolate reductase type V


Mass: 17547.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dhfrV / Plasmid: pET24a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P11731, dihydrofolate reductase
#2: Chemical ChemComp-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N4O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 23% to 25% PEG3350, 0.1M Mes pH 6.0, 0.3M LiSO4 and 2mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.61→99.53 Å / Num. obs: 13057 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.09 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.074 / Net I/σ(I): 7.9
Reflection shellResolution: 2.61→2.73 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1579 / CC1/2: 0.591 / Rpim(I) all: 0.497 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RX2

1rx2


Resolution: 2.61→99.53 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.801 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.562 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.224 742 5.7 %RANDOM
Rwork0.1774 ---
obs0.18 12280 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.85 Å2 / Biso mean: 42.102 Å2 / Biso min: 22.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.81 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: final / Resolution: 2.61→99.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 126 12 2608
Biso mean--55.37 35.64 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132668
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172432
X-RAY DIFFRACTIONr_angle_refined_deg1.891.6413644
X-RAY DIFFRACTIONr_angle_other_deg1.2871.5725598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4015312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68723.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.59315412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.18158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
Refine LS restraints NCS

Ens-ID: 1 / Number: 4634 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.61→2.678 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 74 -
Rwork0.287 897 -
all-971 -
obs--98.68 %

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