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- PDB-1vie: STRUCTURE OF DIHYDROFOLATE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1vie
TitleSTRUCTURE OF DIHYDROFOLATE REDUCTASE
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / NADP / TRIMETHOPRIM RESISTANCE / METHOTREXATE RESISTANCE / ONE-CARBON METABOLISM / PLASMID
Function / homology
Function and homology information


response to methotrexate / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / response to xenobiotic stimulus / response to antibiotic
Similarity search - Function
Dihydrofolate reductase, type II / R67 dihydrofolate reductase / SH3 type barrels. - #60 / Mechanosensitive ion channel MscS, beta-domain superfamily / Electron transport accessory-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Dihydrofolate reductase type 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
AuthorsNarayana, N. / Matthews, D.A. / Howell, E.E. / Xuong, N.-H.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site.
Authors: Narayana, N. / Matthews, D.A. / Howell, E.E. / Nguyen-huu, X.
#1: Journal: Adv.Exp.Med.Biol. / Year: 1993
Title: Does R67 Dihydrofolate Reductase Possess a Proton Donor?
Authors: Holland, J.C. / Linn, C.E. / Digiammarino, E. / Nichols, R. / Howell, E.E.
#2: Journal: Biochemistry / Year: 1991
Title: Construction of a Synthetic Gene for an R-Plasmid-Encoded Dihydrofolate Reductase and Studies on the Role of the N-Terminus in the Protein
Authors: Reece, L.J. / Nichols, R. / Ogden, R.C. / Howell, E.E.
#3: Journal: Biochemistry / Year: 1986
Title: Crystal Structure of a Novel Trimethoprim-Resistant Dihydrofolate Reductase Specified in Escherichia Coli by R-Plasmid R67
Authors: Matthews, D.A. / Smith, S.L. / Baccanari, D.P. / Burchall, J.J. / Oatley, S.J. / Kraut, J.
#4: Journal: J.Biol.Chem. / Year: 1979
Title: The Amino Acid Sequence of the Trimethoprim-Resistant Dihydrofolate Reductase Specified in Escherichia Coli by R-Plasmid R67
Authors: Stone, D. / Smith, S.L.
#5: Journal: Br.Med.J. / Year: 1972
Title: Trimethoprim Resistance Determined by R Factors
Authors: Fleming, M.P. / Datta, N. / Gruneberg, R.N.
History
DepositionOct 3, 1996Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)6,7331
Polymers6,7331
Non-polymers00
Water1,04558
1
A: DIHYDROFOLATE REDUCTASE

A: DIHYDROFOLATE REDUCTASE

A: DIHYDROFOLATE REDUCTASE

A: DIHYDROFOLATE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)26,9304
Polymers26,9304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556y,x,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)68.740, 68.740, 52.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein DIHYDROFOLATE REDUCTASE / R67 DHFR


Mass: 6732.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Strain: TMP-RESISTANT, CONTAINING R67 DHFR OVERPRODUCING PLASMID PLZ1
Gene: SYNTHETIC GENE / Plasmid details: PLZ1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00383, dihydrofolate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Compound detailsR67 PLASMID-ENCODED DHFR HAS 78 AMINO ACID RESIDUES. THE PRESENT STUDY DESCRIBES THE TRUNCATED FORM ...R67 PLASMID-ENCODED DHFR HAS 78 AMINO ACID RESIDUES. THE PRESENT STUDY DESCRIBES THE TRUNCATED FORM OF R67 DHFR (62 RESIDUES) OBTAINED BY CLEAVING THE FULL-LENGTH PROTEIN AT PHE 16 USING CHYMOTRYPSIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALS WERE GROWN FROM HANGING- DROPS CONTAINING PROTEIN AT A FINAL CONCENTRATION OF ABOUT 15 MG/ML IN 100 MM TRIS-HCL BUFFER AT PH 7.5 AND 25% 2-METHYL-2,4-PENTANEDIOL (MPD). DROPS WERE ...Details: CRYSTALS WERE GROWN FROM HANGING- DROPS CONTAINING PROTEIN AT A FINAL CONCENTRATION OF ABOUT 15 MG/ML IN 100 MM TRIS-HCL BUFFER AT PH 7.5 AND 25% 2-METHYL-2,4-PENTANEDIOL (MPD). DROPS WERE EQUILIBRATED AGAINST A RESERVOIR CONTAINING 100 MM KH2PO4 BUFFER AT PH 6.8 AND 50% MPD., vapor diffusion - hanging drop
PH range: 6.8-7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
2100 mMTris-HCl1drop
325 %MPD1drop
4100 mMpotassium phosphate1reservoir
550 %MPD1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 15, 1991
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. obs: 7060 / % possible obs: 98 % / Observed criterion σ(I): 4 / Redundancy: 4 % / Biso Wilson estimate: 10.4 Å2 / Rsym value: 0.036 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.1095 / % possible all: 97
Reflection
*PLUS
Rmerge(I) obs: 0.036

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
UCSDdata reduction
UCSDdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.192 --
obs0.192 6732 94 %
Displacement parametersBiso mean: 18.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms457 0 0 58 515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d16.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16.8

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