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- PDB-6cqa: E. coli DHFR complex with inhibitor AMPQD -

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Basic information

Entry
Database: PDB / ID: 6cqa
TitleE. coli DHFR complex with inhibitor AMPQD
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / dihydrofolate reductase / inhibitor / complex
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PQD / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsCao, H. / Rodrigues, J. / Benach, J. / Wasserman, S. / Morisco, L. / Koss, J. / Shakhnovich, E. / Skolnick, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118039 United States
CitationJournal: Commun Biol / Year: 2018
Title: The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release.
Authors: Cao, H. / Gao, M. / Zhou, H. / Skolnick, J.
History
DepositionMar 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

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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)19,3454
Polymers18,8481
Non-polymers4963
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.651, 64.651, 215.726
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Dihydrofolate reductase


Mass: 18848.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PQD / 7-[(3-aminophenyl)methyl]-7H-pyrrolo[3,2-f]quinazoline-1,3-diamine


Mass: 304.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: 3.61 Å3/Da / Density % sol: 65.94 %
Description: Long and thick rod shape, with longest dimension of 0.05-0.5mm
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 8-10mg/ml protein with 80uM AMPQD and 0.5mM NADPH in 50mM HEPES pH 7.3, 100mM NaCl (concentrated after dialysis), mixed at 1:1 v/v ratio with reservoir solution of 0.1M Citrate pH 3.5, 15% ...Details: 8-10mg/ml protein with 80uM AMPQD and 0.5mM NADPH in 50mM HEPES pH 7.3, 100mM NaCl (concentrated after dialysis), mixed at 1:1 v/v ratio with reservoir solution of 0.1M Citrate pH 3.5, 15% PEG6000, 150mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 6, 2018 / Details: Diamond(111)
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.94→34.175 Å / Num. obs: 17823 / % possible obs: 85.2 % / Redundancy: 14.057 % / Biso Wilson estimate: 53.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.132 / Χ2: 1.061 / Net I/σ(I): 15.81 / Num. measured all: 250532
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.94-2.052.4094.4880.2311980.1375.48736.6
2.05-2.194.7223.8630.4223010.1544.33174
2.19-2.377.6752.6730.7926890.5352.86592.6
2.37-2.612.9271.4182.1326850.9521.47699.9
2.6-2.920.8710.8126.0324400.9860.832100
2.9-3.3521.0080.29215.5721860.9970.299100
3.35-4.120.5450.136.9618850.9990.102100
4.1-5.819.780.0560.28151310.051100
5.8-34.17517.2050.03368.1992610.03499.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7dfr

7dfr


Resolution: 2.2→34.175 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.96
RfactorNum. reflection% reflection
Rfree0.2592 2455 10.14 %
Rwork0.2232 --
obs0.2269 13920 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.76 Å2 / Biso mean: 69.6 Å2 / Biso min: 40.46 Å2
Refinement stepCycle: final / Resolution: 2.2→34.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 47 39 1353
Biso mean--65.4 65.51 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061335
X-RAY DIFFRACTIONf_angle_d1.0091820
X-RAY DIFFRACTIONf_chiral_restr0.035189
X-RAY DIFFRACTIONf_plane_restr0.005234
X-RAY DIFFRACTIONf_dihedral_angle_d13.396480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.24250.4921900.486776785759
2.2425-2.28820.4808960.4521904100072
2.2882-2.3380.42261300.40921051118183
2.338-2.39230.43891400.4081204134494
2.3923-2.45210.38661410.32691253139499
2.4521-2.51840.34811430.32441261140499
2.5184-2.59250.36031360.29871296143299
2.5925-2.67620.31631460.30281264141099
2.6762-2.77180.32451410.29851248138999
2.7718-2.88270.35051360.280212951431100
2.8827-3.01380.31111430.263812641407100
3.0138-3.17260.26641450.252312841429100
3.1726-3.37120.27521450.234412741419100
3.3712-3.63120.29541470.209812881435100
3.6312-3.99620.23051430.197212691412100
3.9962-4.57320.22111490.158112721421100
4.5732-5.75730.18631410.166912781419100
5.7573-34.17950.19581430.192712891432100

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