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- PDB-1dr1: 2.2 ANGSTROMS CRYSTAL STRUCTURE OF CHICKEN LIVER DIHYDROFOLATE RE... -

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Basic information

Entry
Database: PDB / ID: 1dr1
Title2.2 ANGSTROMS CRYSTAL STRUCTURE OF CHICKEN LIVER DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADP+ AND BIOPTERIN
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


tetrahydrofolate metabolic process / response to methotrexate / dihydrofolate metabolic process / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding ...tetrahydrofolate metabolic process / response to methotrexate / dihydrofolate metabolic process / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mRNA binding / mitochondrion
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
7,8-DIHYDROBIOPTERIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMctigue, M.A. / Davies /II, J.F. / Kaufman, B.T. / Xuong, N.-H. / Kraut, J.
Citation
Journal: Biochemistry / Year: 1992
Title: Crystal structure of chicken liver dihydrofolate reductase complexed with NADP+ and biopterin.
Authors: McTigue, M.A. / Davies 2nd., J.F. / Kaufman, B.T. / 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: Derived calculations / 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 / pdbx_struct_special_symmetry / 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 21-26 (NLPWPP) FORM LEFT-HANDED POLYPROLINE HELIX. RESIDUES 108 AND 109 PARTICIPATE ...HELIX RESIDUES 21-26 (NLPWPP) FORM LEFT-HANDED POLYPROLINE HELIX. RESIDUES 108 AND 109 PARTICIPATE IN BOTH HELIX EP AND BETA STRAND E.
Remark 700SHEET RESIDUES 110 AND 111 FORM A BETA-BULGE IN STRAND E. RESIDUES 115 AND 116 FORM A BETA-BULGE IN ...SHEET RESIDUES 110 AND 111 FORM A BETA-BULGE IN STRAND E. RESIDUES 115 AND 116 FORM A BETA-BULGE IN STRAND E. RESIDUES 172 AND 175 PARTICIPATE IN BOTH TIGHT-TURN 8 AND BETA STRANDS 7 AND 9. 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7034
Polymers21,6801
Non-polymers1,0233
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DIHYDROFOLATE REDUCTASE
hetero molecules

A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4058
Polymers43,3602
Non-polymers2,0456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4550 Å2
ΔGint-40 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.440, 48.310, 64.260
Angle α, β, γ (deg.)90.00, 125.10, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES 21-26 (NLPWPP) FORM LEFT-HANDED POLYPROLINE HELIX.
2: RESIDUE TYR 31 EXISTS IN TWO CONFORMATIONS. / 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 9.948
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

#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
#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 / Nicotinamide adenine dinucleotide phosphate


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


Mass: 239.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N5O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 53.02 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlcDHFR1drop
22 mMNADP+1drop
310 mMcalcium acetate1drop
42 mMdithiothreitol1drop
520 mMTris-HCl1drop
623 %(v/v)ethanol1reservoir
710 mMcalcium acetate1reservoir
820 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 10688 / % possible obs: 91.2 % / Rmerge(I) obs: 0.022

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.14 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 66 133 1688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
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
Refinement
*PLUS
Highest resolution: 2.2 Å / Rfactor obs: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.7 Å2
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.04

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