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- PDB-1vif: STRUCTURE OF DIHYDROFOLATE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1vif
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
FOLIC ACID / Dihydrofolate reductase type 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 1.8 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 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)7,1742
Polymers6,7331
Non-polymers4411
Water79344
1
A: DIHYDROFOLATE REDUCTASE
hetero molecules

A: DIHYDROFOLATE REDUCTASE
hetero molecules

A: DIHYDROFOLATE REDUCTASE
hetero molecules

A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6968
Polymers26,9304
Non-polymers1,7664
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)68.750, 68.750, 52.590
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: PLZ1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00383, dihydrofolate reductase
#2: Chemical ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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.
Nonpolymer detailsTHE TWO MUTUALLY EXCLUSIVE FOLATE MOLECULES AT 1/4 OCCUPANCY ARE LABELLED AS FOL 1 WITH ALTERNATE ...THE TWO MUTUALLY EXCLUSIVE FOLATE MOLECULES AT 1/4 OCCUPANCY ARE LABELLED AS FOL 1 WITH ALTERNATE LOCATIONS A AND B. HOWEVER, DENSITY IS SEEN ONLY FOR THE PTERIDINE PORTION. THUS ATOMIC COORDINATES FOR THE PARA AMINO BENZOYL GLUTAMATE MOIETY ARE NOT FOUND IN THIS ENTRY. THE WATER MOLECULE 124 HAS 1/2 OCCUPANCY. IT OCCUPIES THE POSITION OF O4 OF THE PTERIDINE RING IN ITS ABSENCE.

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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: 8
Details: CRYSTALS WERE GROWN FROM HANGING- DROPS CONTAINING PROTEIN AT A FINAL CONCENTRATION OF ABOUT 18 MG/ML, 30 MM FOLATE, 40 MM BICINE BUFFER AT PH 8.0 AND 18% 2-METHYL-2,4-PENTANE DIOL (MPD). ...Details: CRYSTALS WERE GROWN FROM HANGING- DROPS CONTAINING PROTEIN AT A FINAL CONCENTRATION OF ABOUT 18 MG/ML, 30 MM FOLATE, 40 MM BICINE BUFFER AT PH 8.0 AND 18% 2-METHYL-2,4-PENTANE DIOL (MPD). DROPS WERE EQUILIBRATED AGAINST A RESERVOIR CONTAINING 100 MM KH2PO4 BUFFER AT PH 6.8 AND 50% MPD. THE CRYSTALS WERE FURTHER SOAKED IN 100 MM FOLATE FOR 3 DAYS., vapor diffusion - hanging drop
PH range: 6.8-8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 mg/mlprotein1drop
240 mMbicine1drop
318 %MPD1drop
4100 mMpotassium phosphate1reservoir
550 %MPD1reservoir
630 mMfolate1drop

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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: Mar 15, 1992
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 6094 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 10.7 Å2 / Rsym value: 0.055 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.16 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.055

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
UCSDdata reduction
UCSDdata scaling
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: PDB ENTRY 1VIE

1vie


Resolution: 1.8→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.176 --
obs0.176 6040 100 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms457 0 26 44 527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.5
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_deg18.5

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