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- PDB-4dfr: CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DI... -

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Entry
Database: PDB / ID: 4dfr
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


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
METHOTREXATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
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: 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.
#2: 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.
#3: 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.
#4: 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.
#5: 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.
#6: 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.
#7: 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.
#8: 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.
#9: 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.
#10: 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
DepositionJun 25, 1982Processing site: BNL
SupersessionOct 21, 1982ID: 2DFR
Revision 1.0Oct 21, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
B: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0617
Polymers36,0412
Non-polymers1,0205
Water7,710428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.220, 93.220, 73.560
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 8. / 2: SEE REMARK 9. / 3: SEE REMARK 10. / 4: SEE REMARK 11.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.92116, -0.37966, 0.636818), (-0.34623, 0.69913, -0.62558), (0.177743, -0.605172, -0.775593)
Vector: 59.21707, 47.40033, 96.59826)
DetailsTHE MTRIX TRANSFORMATION PRESENTED BELOW WILL SUPERIMPOSE MOLECULE B ON MOLECULE A.

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Components

#1: Protein DIHYDROFOLATE REDUCTASE /


Mass: 18020.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MTX / METHOTREXATE / Methotrexate


Mass: 454.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 142 IS LISTED AS ASN IN THE SEQUENCE PAPER (SEE REFERENCE 9 ABOVE). THE X-RAY STRUCTURE ...RESIDUE 142 IS LISTED AS ASN IN THE SEQUENCE PAPER (SEE REFERENCE 9 ABOVE). THE X-RAY STRUCTURE SUGGESTS IT IS ASP (EVIDENCE IS INTERMOLECULAR SALT-LINKAGE TO AN ARG).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %ethanol11
20.01 Mhistidine hydorochloride11
35 mMcalcium acetate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 32554 / % possible obs: 88 %

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Processing

RefinementRfactor Rwork: 0.155 / Highest resolution: 1.7 Å
Details: MOLECULE DESIGNATED AS CHAIN B BELOW IS PREFERRED FOR STRUCTURAL COMPARISONS BECAUSE IT IS MORE COMPLETE AND LESS PERTURBED BY INTERMOLECULAR CONTACTS. ALTERNATE LOCATIONS *A* AND *B* ARE ...Details: MOLECULE DESIGNATED AS CHAIN B BELOW IS PREFERRED FOR STRUCTURAL COMPARISONS BECAUSE IT IS MORE COMPLETE AND LESS PERTURBED BY INTERMOLECULAR CONTACTS. ALTERNATE LOCATIONS *A* AND *B* ARE PARTIALLY OCCUPIED CONFORMATIONS FOR RESIDUES SER A 64, SER A 150, HIS B 45, SER B 64 AND ASP B 122. IN ALL CASES, *A* IS BELIEVED TO BE THE MAJOR CONFORMER. NEITHER THE OCCUPANCIES NOR THE THERMAL PARAMETERS SHOULD BE CONSIDERED AS RELIABLE.
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 69 428 3005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.07
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 1.7 Å / Num. reflection all: 32554 / Rfactor obs: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS

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