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- PDB-3dfr: CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DI... -

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Basic information

Entry
Database: PDB / ID: 3dfr
TitleCRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / OXIDO-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, subunit A / Dihydrofolate Reductase, subunit A / 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
METHOTREXATE / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsFilman, D.J. / Matthews, D.A. / Bolin, J.T. / Kraut, J.
Citation
Journal: J.Biol.Chem. / Year: 1982
Title: Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.
Authors: Bolin, J.T. / Filman, D.J. / Matthews, D.A. / Hamlin, R.C. / Kraut, J.
#1: Journal: J.Biol.Chem. / Year: 1982
Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. II. Environment of Bound Nadph and Implications for Catalysis
Authors: Filman, D.J. / Bolin, J.T. / Matthews, D.A. / Kraut, J.
#2: Journal: J.Biol.Chem. / Year: 1982
Title: Crystal Structure of Avian Dihydrofolate Reductase Containing Phenyltriazine and Nadph
Authors: Volz, K.W. / Matthews, D.A. / Alden, R.A. / Freer, S.T. / Hansch, C. / Kaufman, B.T. / Kraut, J.
#3: Journal: Biochemistry / Year: 1979
Title: Interpretation of Nuclear Magnetic Resonance Spectra for Lactobacillus Casei Dihydrofolate Reductase Based on the X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex
Authors: Matthews, D.A.
#4: Journal: J.Biol.Chem. / Year: 1979
Title: Dihydrofolate Reductase from Lactobacillus Casei. Stereochemistry of Nadph Binding
Authors: Matthews, D.A. / Alden, R.A. / Freer, S.T. / Xuong, N.-H. / Kraut, J.
#5: Journal: J.Biol.Chem. / Year: 1978
Title: Dihydrofolate Reductase from Lactobacillus Casei. X-Ray Structure of the Enzyme-Methotrexate-Nadph Complex
Authors: Matthews, D.A. / Alden, R.A. / Bolin, J.T. / Filman, D.J. / Freer, S.T. / Hamlin, R. / Hol, W.G.J. / Kisliuk, R.L. / Pastore, E.J. / Plante, L.T. / Xuong, N.-H. / Kraut, J.
#6: Journal: Science / Year: 1977
Title: Dihydrofolate Reductase. X-Ray Structure of the Binary Complex with Methotrexate
Authors: Matthews, D.A. / Alden, R.A. / Bolin, J.T. / Freer, S.T. / Hamlin, R. / Xuong, N. / Kraut, J. / Poe, M. / Williams, M. / Hoogsteen, K.
#7: Journal: J.Biol.Chem. / Year: 1970
Title: Properties of Thymidylate Synthetase from Dichloromethotrexate-Resistant Lactobacillus Casei
Authors: Crusberg, T.C. / Leary, R. / Kisliuk, R.L.
History
DepositionJun 25, 1982Processing site: BNL
SupersessionOct 21, 1982ID: 1DFR
Revision 1.0Oct 21, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Structure summary
Category: pdbx_database_status / struct_conf ...pdbx_database_status / struct_conf / struct_conf_type / struct_keywords
Item: _pdbx_database_status.process_site / _struct_keywords.text
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)19,5463
Polymers18,3461
Non-polymers1,2002
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.860, 71.860, 93.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: SEE REMARK 6. / 2: SEE REMARK 7.

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Components

#1: Protein DIHYDROFOLATE REDUCTASE


Mass: 18345.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / References: UniProt: P00381, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.57 %
Crystal grow
*PLUS
pH: 7.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
155 %satammonium sulfate11
20.01 MTris11

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 24380 / % possible obs: 92 % / Rmerge(I) obs: 0.06

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Processing

RefinementRfactor Rwork: 0.152 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 81 264 1639
Refinement
*PLUS
Num. reflection obs: 24380
Solvent computation
*PLUS
Displacement parameters
*PLUS

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