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- PDB-2dhf: CRYSTAL STRUCTURES OF RECOMBINANT HUMAN DIHYDROFOLATE REDUCTASE C... -

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Basic information

Entry
Database: PDB / ID: 2dhf
TitleCRYSTAL STRUCTURES OF RECOMBINANT HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH FOLATE AND 5-DEAZOFOLATE
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / OXIDO-REDUCTASE
Function / homology
Function and homology information


regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / 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
5-DEAZAFOLIC ACID / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsDavies /II, J.F. / Kraut, J.
Citation
Journal: Biochemistry / Year: 1990
Title: Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate.
Authors: Davies 2nd., J.F. / Delcamp, T.J. / Prendergast, N.J. / Ashford, V.A. / Freisheim, J.H. / Kraut, J.
#1: Journal: Biochemistry / Year: 1988
Title: Expression and Site-Directed Mutagenesis of Human Dihydrofolate Reductase
Authors: Prendergast, N.J. / Delcamp, T.J. / Smith, P.L. / Freisheim, J.H.
History
DepositionOct 25, 1989Processing site: BNL
Revision 1.0Jul 15, 1990Provider: 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 / 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 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX IN EACH CHAIN, RESIDUES ASP 21 - LEU 22 - PRO 23 - TRP 24 - PRO 25 - PRO 26 ARE IN LEFT- ...HELIX IN EACH CHAIN, RESIDUES ASP 21 - LEU 22 - PRO 23 - TRP 24 - PRO 25 - PRO 26 ARE IN LEFT-HANDED POLYPROLINE HELIX CONFORMATION.
Remark 700SHEET THE FOLLOWING REMARKS APPLY TO EACH CHAIN. IN THE *HELIX*, *SHEET* AND *TURN* RECORDS BELOW, ...SHEET THE FOLLOWING REMARKS APPLY TO EACH CHAIN. IN THE *HELIX*, *SHEET* AND *TURN* RECORDS BELOW, AN *A* OR *B* HAS BEEN APPENDED TO THE NAMES USED IN THIS REMARK TO DISTINGUISH CHAINS. RESIDUE GLN 102 PARTICIPATES IN BOTH HELIX E AND EP. RESIDUES LYS 108 AND VAL 109 PARTICIPATE IN BOTH HELIX EP AND STRAND E. RESIDUE GLU 172 IS IN TIGHT-TURN 8 AND BETA STRAND G. RESIDUE ILE 175 IS IN TIGHT-TURN 8 AND BETA STRAND H. RESIDUES ASP 110 - MET 111 FORM A BETA-BULGE IN STRAND E. RESIDUES VAL 115 - GLY 116 FORM A BETA-BULGE IN STRAND E. TIGHT TURN 7 DISRUPTS STRAND G. THIS IS REPRESENTED ON THE SHEET RECORDS BELOW BY PRESENTING THE SHEET TWICE WITH STRAND 8 DIFFERENT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,5804
Polymers42,6992
Non-polymers8812
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.100, 38.500, 76.800
Angle α, β, γ (deg.)93.90, 91.40, 111.50
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUES PRO A 66 AND PRO B 66 ARE CIS PROLINES.
2: IN EACH CHAIN, THE PEPTIDE BOND LINKING GLY 116 TO GLY 117 IS IN THE CIS CONFORMATION.

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Components

#1: Protein DIHYDROFOLATE REDUCTASE /


Mass: 21349.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00374, dihydrofolate reductase
#2: Chemical ChemComp-DZF / 5-DEAZAFOLIC ACID


Mass: 440.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.025 Mpotassium phosphate1drop
21 mMdithioerythritol1drop
310 mg/mlenzyme1drop
50.17 Msodium acetate1reservoir
620 %(w/v)PEG40001reservoir
77 %(v/v)ethanol1reservoir
4folate1drop3-fold molar ecess of substrate to enzyme

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 15545 / % possible obs: 95 % / Rmerge(I) obs: 0.05

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.194 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 64 111 3123
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.018
X-RAY DIFFRACTIONp_angle_d0.0350.023
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.842
X-RAY DIFFRACTIONp_mcangle_it6.413
X-RAY DIFFRACTIONp_scbond_it5.692
X-RAY DIFFRACTIONp_scangle_it7.683
X-RAY DIFFRACTIONp_plane_restr0.0150.013
X-RAY DIFFRACTIONp_chiral_restr0.3370.2
X-RAY DIFFRACTIONp_singtor_nbd0.2220.4
X-RAY DIFFRACTIONp_multtor_nbd0.290.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2270.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.35
X-RAY DIFFRACTIONp_staggered_tor25.915
X-RAY DIFFRACTIONp_orthonormal_tor23.115
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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