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- PDB-1dr4: CRYSTAL STRUCTURES OF ORGANOMERCURIAL-ACTIVATED CHICKEN LIVER DIH... -

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Entry
Database: PDB / ID: 1dr4
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 / : / 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: 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 / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.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.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. 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 172 AND 175 PARTICIPATE IN BOTH TIGHT-TURN 8 AND BETA STRANDS 7 AND 9.

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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)22,9035
Polymers21,6801
Non-polymers1,2234
Water1,36976
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)45,80610
Polymers43,3602
Non-polymers2,4478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4560 Å2
ΔGint-41 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.080, 48.290, 64.320
Angle α, β, γ (deg.)90.00, 124.80, 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 6.474
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, 80 molecules

#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Chemical ChemComp-HBI / 7,8-DIHYDROBIOPTERIN


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


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCYSTEINE 11 HAS A MERCURY ATOM COVALENTLY BOUND TO SG IN TWO CONFORMATIONS. THE METHYL GROUP BOUND ...CYSTEINE 11 HAS A MERCURY ATOM COVALENTLY BOUND TO SG IN TWO CONFORMATIONS. THE METHYL GROUP BOUND TO THE MERCURY ATOM IS NOT INCLUDED AS IT IS DISORDERED.

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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: 53.03 %
Crystal grow
*PLUS
pH: 5.5 / Method: other
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.15 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 67 76 1623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
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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