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- PDB-1dr6: CRYSTAL STRUCTURES OF ORGANOMERCURIAL-ACTIVATED CHICKEN LIVER DIH... -

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Entry
Database: PDB / ID: 1dr6
TitleCRYSTAL STRUCTURES OF ORGANOMERCURIAL-ACTIVATED CHICKEN LIVER DIHYDROFOLATE REDUCTASE COMPLEXES
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE
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
7,8-DIHYDROBIOPTERIN / MERCURIBENZOIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsMctigue, M.A. / Davies /II, J.F. / Kaufman, B.T. / Xuong, N.-H. / Kraut, J.
Citation
Journal: To be Published
Title: Crystal Structures of Organomercurial-Activated Chicken Liver Dihydrofolate Reductase Complexes
Authors: Mctigue, M.A. / Davies II, J.F. / Kaufman, B.T. / Xuong, N.-H. / Kraut, J.
#1: Journal: Biochemistry / Year: 1990
Title: Crystal Structures of Recombinant Human Dihydrofolate Reductase Complexed with Folate and 5-Deazafolate
Authors: Davies II, J.F. / Delcamp, T.J. / Prendergast, N.J. / Ashford, V.A. / Freisheim, J.H. / Kraut, J.
#2: Journal: J.Biol.Chem. / Year: 1985
Title: Refined Crystal Structure 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.
#3: 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.
#4: 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.
#5: 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
DepositionMar 14, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 7, 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_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX RESIDUES 21-26 (NLPWPP) FORM A LEFT-HANDED POLYPROLINE HELIX. RESIDUES LYS 108 AND VAL 109 ...HELIX RESIDUES 21-26 (NLPWPP) FORM A LEFT-HANDED POLYPROLINE HELIX. RESIDUES LYS 108 AND VAL 109 PARTICIPATE IN BOTH HELIX EP AND BETA STRAND E. RESIDUES 108 AND 109 PARTICIPATE IN BOTH HELIX EP AND BETA STRAND E.
Remark 700SHEET RESIDUES ASP 110 AND MET 111 FORM A BETA-BULGE IN STRAND E. RESIDUES VAL 115 AND GLY 116 FORM ...SHEET RESIDUES ASP 110 AND MET 111 FORM A BETA-BULGE IN STRAND E. RESIDUES VAL 115 AND GLY 116 FORM A BETA-BULGE IN STRAND E. TIGHT TURN 7 (RESIDUES 162-165) DISRUPT LAST STRAND OF SHEET INTO 2 STRANDS 8 AND 9. THIS STRAND IS CONTINUOUS IN (E. COLI). A BETA BULGE IS PRESENT HERE IN (L. CASEI). RESIDUES GLU 172 AND ILE 175 PARTICIPATE IN BOTH TIGHT-TURN 8 AND BETA STRANDS 7 AND 9.

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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)23,0245
Polymers21,6801
Non-polymers1,3444
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.720, 48.740, 63.870
Angle α, β, γ (deg.)90.00, 124.70, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: SEE REMARK 6.
2: RESIDUES 21-26 (NLPWPP) FORM LEFT-HANDED POLYPROLINE HELIX.
3: CIS PROLINE - PRO 66
4: RESIDUES 108 AND 109 PARTICIPATE IN BOTH HELIX EP AND BETA STRAND E.
5: RESIDUES 110 AND 111 FORM A BETA-BULGE IN STRAND E. / 6: RESIDUES 115 AND 116 FORM A BETA-BULGE IN STRAND E.
7: PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION GLY 116 - GLY 117 3.713
8: TIGHT TURN 7 (RESIDUES 162-165) DISRUPT LAST STRAND OF SHEET INTO 2 STRANDS 8 AND 9. THIS STRAND IS CONTINUOUS IN E. COLI. A BETA BULGE IS PRESENT HERE IN L. CASEI.
9: RESIDUES 172 AND 175 PARTICIPATE IN BOTH TIGHT-TURN 8 AND BETA STRANDS 7 AND 9.
10: RESIDUE 200 (CALCIUM ION) LIES ON THE CRYSTALLOGRAPHIC TWO-FOLD AT ONE-HALF OCCUPANCY.
Components on special symmetry positions
IDModelComponents
11A-200-

CA

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Components

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Protein , 1 types, 1 molecules A

#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) / Organ: LIVER / References: UniProt: P00378, dihydrofolate reductase

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Non-polymers , 5 types, 78 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-HBI / 7,8-DIHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N5O3
#5: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.62 Å3/Da / Density % sol: 53 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.141 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 77 74 1644
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
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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