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- PDB-8dfr: REFINED CRYSTAL STRUCTURES OF CHICKEN LIVER DIHYDROFOLATE REDUCTA... -

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Entry
Database: PDB / ID: 8dfr
TitleREFINED CRYSTAL STRUCTURES OF CHICKEN LIVER DIHYDROFOLATE REDUCTASE. 3 ANGSTROMS APO-ENZYME AND 1.7 ANGSTROMS NADPH HOLO-ENZYME COMPLEX
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE(CHNH(D)-NAD+ OR NADP+(A))
Function / homology
Function and homology information


tetrahydrofolate metabolic process / response to methotrexate / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mRNA binding / mitochondrion
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
Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsMatthews, D.A. / Oatley, S.J. / Burridge, J. / Kaufman, B.T. / Xuong, N.-H. / Kraut, J.
Citation
Journal: To be Published
Title: Refined Crystal Structures of Chicken Liver Dihydrofolate Reductase. 3 Angstroms Apo-Enzyme and 1.7 Angstroms Nadph Holo-Enzyme Complex
Authors: Davies /II, J.F. / Matthews, D.A. / Oatley, S.J. / Kaufman, B.T. / Xuong, N.-H. / Kraut, J.
#1: Journal: J.Biol.Chem. / Year: 1985
Title: Refined Crystal Structures of Escherichia Coli and Chicken Liver Dihydrofolate Reductase Containing Bound Trimethoprim
Authors: Matthews, D.A. / Bolin, J.T. / Burridge, J.M. / Filman, D.J. / Volz, K.W. / Kaufman, B.T. / Beddell, C.R. / Champness, J.N. / Stammers, D.K. / Kraut, J.
#2: Journal: J.Biol.Chem. / Year: 1985
Title: Dihydrofolate Reductase. The Stereochemistry of Inhibitor Selectivity
Authors: Matthews, D.A. / Bolin, J.T. / Burridge, J.M. / Filman, D.J. / Volz, K.W. / 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: 1980
Title: Primary Structure of Chicken Liver Dihydrofolate Reductase
Authors: Kumar, A.A. / Blankenship, D.T. / Kaufman, B.T. / Freisheim, J.H.
History
DepositionMay 30, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: 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 1.4Feb 14, 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_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_atom_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX RESIDUES 21 THROUGH 26 FORM A NEARLY-IDEAL LEFT-HANDED POLYPROLINE HELIX WITH SEQUENCE ASN- ...HELIX RESIDUES 21 THROUGH 26 FORM A NEARLY-IDEAL LEFT-HANDED POLYPROLINE HELIX WITH SEQUENCE ASN-LEU-PRO-TRP-PRO-PRO. RESIDUE 102 PARTICIPATES IN BOTH HELIX E AND HELIX EP. RESIDUES 108 AND 109 PARTICIPATE IN BOTH HELIX EP AND BETA STRAND E.
Remark 700SHEET THIS PROTEIN CONTAINS ONE EIGHT-STRANDED SHEET. THE LAST STRAND IS INTERRUPTED BY A BETA- ...SHEET THIS PROTEIN CONTAINS ONE EIGHT-STRANDED SHEET. THE LAST STRAND IS INTERRUPTED BY A BETA-BLOWOUT OF EIGHT RESIDUES, FOUR OF WHICH (162 - 165) FORM A BETA-TURN. THIS IS REPRESENTED BY PRESENTING THE SHEET TWICE WITH DIFFERENT LAST STRANDS. IN E. COLI DFR THIS STRAND IS CONTINUOUS. IN L. CASEI DFR A BETA BULGE IS PRESENT. RESIDUES 172 AND 175 PARTICIPATE IN BOTH TIGHT TURN 8 AND BETA STRANDS 7 AND 9. RESIDUES 115 AND 116 FORM A BETA-BULGE IN STRAND E. RESIDUES 110 AND 111 FORM A BETA-BULGE IN STRAND E.

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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)22,4653
Polymers21,6801
Non-polymers7852
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.070, 47.960, 64.310
Angle α, β, γ (deg.)90.00, 124.84, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUE 66 IS A CIS PROLINE.
2: THE PEPTIDE BOND JOINING RESIDUES GLY 116 AND GLY 117 IS IN THE CIS CONFORMATION.
Components on special symmetry positions
IDModelComponents
11A-200-

CA

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Components

#1: Protein DIHYDROFOLATE REDUCTASE


Mass: 21679.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00378, dihydrofolate reductase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.6 Å3/Da / Density % sol: 52.67 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.188 / Highest resolution: 1.7 Å
Details: CYS 11 APPEARS TO BE OXIDIZED TO SO3H (CYSTEIC ACID) DURING X-RAY DATA COLLECTION. CYSTEIC ACID WAS APPROXIMATED BY PLACING THREE WATER MOLECULES (HOH 645, HOH 657, AND HOH 674) AROUND THE ...Details: CYS 11 APPEARS TO BE OXIDIZED TO SO3H (CYSTEIC ACID) DURING X-RAY DATA COLLECTION. CYSTEIC ACID WAS APPROXIMATED BY PLACING THREE WATER MOLECULES (HOH 645, HOH 657, AND HOH 674) AROUND THE SULFUR OF THE CYSTEINE RESIDUE.
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 49 122 1675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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