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- PDB-2anq: Crystal Structure of E.coli DHFR in complex with NADPH and the in... -

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Basic information

Entry
Database: PDB / ID: 2anq
TitleCrystal Structure of E.coli DHFR in complex with NADPH and the inhibitor compound 10a.
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / protein 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-C1A / : / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsSummerfield, R.L. / Daigle, D.M. / Mayer, S. / Jackson, S.G. / Organ, M. / Hughes, D.W. / Brown, E.D. / Junop, M.S.
CitationJournal: J.Med.Chem. / Year: 2006
Title: A 2.13 A Structure of E. coli Dihydrofolate Reductase Bound to a Novel Competitive Inhibitor Reveals a New Binding Surface Involving the M20 Loop Region
Authors: Summerfield, R.L. / Daigle, D.M. / Mayer, S. / Mallik, D. / Hughes, D.W. / Jackson, S.G. / Sulek, M. / Organ, M.G. / Brown, E.D. / Junop, M.S.
History
DepositionAug 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 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)19,2425
Polymers18,0201
Non-polymers1,2224
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.000, 44.720, 98.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Dihydrofolate reductase


Mass: 18020.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, tmrA / Plasmid: pFW117.1 DHFR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-C1A / (2,5-dimethylbenzene-1,4-diyl)dimethanediyl bis(N-carbamimidoylcarbamimidothioate) / 4-({[(E)-{[(E)-AMINO(IMINO)METHYL]AMINO}(IMINO)METHYL]SULFANYL}METHYL)-2,5-DIMETHYLBENZYL N-[(E)-AMINO(IMINO)METHYL]IMIDOTHIOCARBAMATE


Mass: 366.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N8S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.072 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 6000, imidazole, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 23, 2003 / Details: Mirrors
RadiationMonochromator: Blue confocal optics Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→40.68 Å / Num. all: 12541 / Num. obs: 12305 / % possible obs: 98.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.66 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.071 / Χ2: 0.96 / Net I/σ(I): 8.8 / Scaling rejects: 248
Reflection shellResolution: 1.89→1.96 Å / % possible obs: 98.9 % / Redundancy: 2.69 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.4 / Num. measured obs: 100 / Num. unique all: 1221 / Χ2: 1.19 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata processing
CNSrefinement
PDB_EXTRACT1.601data extraction
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→25 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 770 8.7 %Random
Rwork0.233 ---
all0.2384 8708 --
obs0.2348 8517 96.4 %-
Solvent computationBsol: 57.476 Å2
Displacement parametersBiso mean: 26.565 Å2
Baniso -1Baniso -2Baniso -3
1-2.845 Å20 Å20 Å2
2---7.42 Å20 Å2
3---4.575 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.13→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 74 407 1749
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_ang_deg29.6
X-RAY DIFFRACTIONc_improper_angle_deg1.31
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ligand.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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