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- PDB-5dfr: CRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE RE... -

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Basic information

Entry
Database: PDB / ID: 5dfr
TitleCRYSTAL STRUCTURE OF UNLIGANDED ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE. LIGAND-INDUCED CONFORMATIONAL CHANGES AND COOPERATIVITY IN BINDING
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / OXIDO-REDUCTASE
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic 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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBystroff, C. / Kraut, J.
Citation
Journal: Biochemistry / Year: 1991
Title: Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding.
Authors: Bystroff, C. / Kraut, J.
#1: Journal: Biochemistry / Year: 1990
Title: Crystal Structures of Escherichia Coli Dihydrofolate Reductase. The Nadp+ Holoenzyme and the Folate(Dot)Nadp+ Ternary Complex. Substrate Binding and a Model for the Transition State
Authors: Bystroff, C. / Oatley, S.J. / Kraut, J.
#2: Journal: J.Biol.Chem. / Year: 1982
Title: Crystal Structures of Escherichia Coli and Lactobacillus Casei Dihydrofolate Reductase Refined at 1.7 Angstroms Resolution. I. General Features and Binding of Methotrexate
Authors: Bolin, J.T. / Filman, D.J. / Matthews, D.A. / Hamlin, R.C. / Kraut, J.
#3: Journal: Biochemistry / Year: 1987
Title: Effect of Single Amino Acid Replacements on the Folding and Stability of Dihydrofolate Reductase from Escherichia Coli
Authors: Perry, K.M. / Onuffer, J.J. / Touchette, N.A. / Herndon, C.S. / Gittelman, M.S. / Matthews, C.R. / Chen, J.-T. / Mayer, R.J. / Taira, K. / Benkovic, S.J. / Howell, E.E. / Kraut, J.
#4: 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.
#5: 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.
#6: 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.
#7: 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.
#8: Journal: J.Biol.Chem. / Year: 1979
Title: Proton Magnetic Resonance Studies on Escherichia Coli Dihydrofolate Reductase. Assignment of Histidine C-2 Protons in Binary Complexes with Folates on the Basis of the Crystal Structure with ...Title: Proton Magnetic Resonance Studies on Escherichia Coli Dihydrofolate Reductase. Assignment of Histidine C-2 Protons in Binary Complexes with Folates on the Basis of the Crystal Structure with Methotrexate and on Chemical Modifications
Authors: Poe, M. / Hoogsteen, K. / Matthews, D.A.
#9: 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.
#10: Journal: Biochemistry / Year: 1978
Title: Dihydrofolate Reductase. The Amino Acid Sequence of the Enzyme from a Methotrexate-Resistant Mutant of Escherichia Coli
Authors: Bennett, C.D. / Rodkey, J.A. / Sondey, J.M. / Hirschmann, R.
#11: 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.
#12: Journal: Biochemistry / Year: 1972
Title: Dihydrofolate Reductase. Purification and Characterization of the Enzyme from an Amethopterin-Resistant Mutant of Escherichia Coli
Authors: Poe, M. / Greenfield, N.J. / Hirshfield, J.M. / Williams, M.N. / Hoogsteen, K.
History
DepositionOct 21, 1988Processing site: BNL
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 6, 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)18,1274
Polymers18,0201
Non-polymers1063
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.730, 68.730, 83.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: RESIDUES PRO 21 - LEU 24 ARE WEAK. THERE IS UNINTERPRETED DENSITY ASSOCIATED WITH THE SIDE CHAIN OF PHE 31. RESIDUES 95 - 96 ARE PARTIALLY DISORDERED. VAL 10, GLU 120, ASP 122, AND ASP 127 HAVE ...1: RESIDUES PRO 21 - LEU 24 ARE WEAK. THERE IS UNINTERPRETED DENSITY ASSOCIATED WITH THE SIDE CHAIN OF PHE 31. RESIDUES 95 - 96 ARE PARTIALLY DISORDERED. VAL 10, GLU 120, ASP 122, AND ASP 127 HAVE DISORDERED SIDE CHAINS. THE SIDE CHAIN OF LEU 28, IN THE SUBSTRATE BINDING SITE, APPEARS TO BE PARTIALLY DISORDERED.
2: THE IDENTITY OF IONS 501 THROUGH 503 IS NOT DETERMINED. THEY HAVE TENATIVELY BEEN ASSIGNED AS CHLORINE IONS BASED ON THEIR ELECTRON DENSITY, THE BINDING ENVIRONMENT, AND THE BELIEF THAT CHLORIDE ...2: THE IDENTITY OF IONS 501 THROUGH 503 IS NOT DETERMINED. THEY HAVE TENATIVELY BEEN ASSIGNED AS CHLORINE IONS BASED ON THEIR ELECTRON DENSITY, THE BINDING ENVIRONMENT, AND THE BELIEF THAT CHLORIDE IS THE ONLY NEGATIVELY-CHARGED MONO-ATOMIC ION PRESENT IN THE CRYSTALLIZATION MIXTURE.

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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) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE IDENTITY OF IONS 501 THROUGH 503 IS NOT DETERMINED. THEY HAVE TENATIVELY BEEN ASSIGNED AS ...THE IDENTITY OF IONS 501 THROUGH 503 IS NOT DETERMINED. THEY HAVE TENATIVELY BEEN ASSIGNED AS CHLORINE IONS BASED ON THEIR ELECTRON DENSITY, THE BINDING ENVIRONMENT, AND THE BELIEF THAT CHLORIDE IS THE ONLY NEGATIVELY-CHARGED MONO-ATOMIC ION PRESENT IN THE CRYSTALLIZATION MIXTURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
124 mg/mlprotein1dropunliganded
250 mMsodium/potassium phthalate1drop
350 %(w/w)PEG60001drop
425 %PEG60001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 2.3 Å / Num. all: 63697 / Num. obs: 14169 / Num. measured all: 14730 / Rmerge(I) obs: 0.043

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→20 Å / Rfactor obs: 0.198
Details: THE PAPER CITED ON THE *JRNL* RECORDS ABOVE DISCUSSES THE QUESTION AS TO WHETHER THE PEPTIDE BOND BETWEEN GLY 95 AND GLY 96 IS IN THE CIS OR THE TRANS CONFORMATION. A DISORDERED MODEL IN ...Details: THE PAPER CITED ON THE *JRNL* RECORDS ABOVE DISCUSSES THE QUESTION AS TO WHETHER THE PEPTIDE BOND BETWEEN GLY 95 AND GLY 96 IS IN THE CIS OR THE TRANS CONFORMATION. A DISORDERED MODEL IN WHICH THIS PEPTIDE EXISTS IN BOTH CONFORMERS CANNOT BE RULED OUT. IN THIS ENTRY, HOWEVER, ONLY COORDINATES CORRESPONDING TO THE TRANS CONFORMATION ARE PROVIDED. RESIDUES PRO 21 - LEU 24 ARE WEAK. THERE IS UNINTERPRETED DENSITY ASSOCIATED WITH THE SIDE CHAIN OF PHE 31. RESIDUES GLY 95 - GLY 96 ARE PARTIALLY DISORDERED. VAL 10, GLU 120, ASP 122, AND ASP 127 HAVE DISORDERED SIDE CHAINS. THE SIDE CHAIN OF LEU 28, IN THE SUBSTRATE BINDING SITE, APPEARS TO BE PARTIALLY DISORDERED.
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 3 120 1343
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.02
X-RAY DIFFRACTIONp_angle_d0.0660.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0770.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.4122
X-RAY DIFFRACTIONp_mcangle_it5.8323
X-RAY DIFFRACTIONp_scbond_it5.0882
X-RAY DIFFRACTIONp_scangle_it6.9143
X-RAY DIFFRACTIONp_plane_restr0.0240.02
X-RAY DIFFRACTIONp_chiral_restr0.3470.2
X-RAY DIFFRACTIONp_singtor_nbd0.2290.3
X-RAY DIFFRACTIONp_multtor_nbd0.2350.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2130.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor11.35
X-RAY DIFFRACTIONp_staggered_tor26.515
X-RAY DIFFRACTIONp_orthonormal_tor22.315
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31 Å2

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