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- PDB-2rk2: DHFR R-67 complexed with NADP -

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Basic information

Entry
Database: PDB / ID: 2rk2
TitleDHFR R-67 complexed with NADP
ComponentsDihydrofolate reductase type 2
KeywordsOXIDOREDUCTASE / NADP / asymmetric ligand binding / Antibiotic resistance / Methotrexate resistance / One-carbon metabolism / Trimethoprim resistance
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase type 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKrahn, J.M. / London, R.E.
CitationJournal: Biochemistry / Year: 2007
Title: Crystal structure of a type II dihydrofolate reductase catalytic ternary complex.
Authors: Krahn, J.M. / Jackson, M.R. / DeRose, E.F. / Howell, E.E. / London, R.E.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8305
Polymers6,7331
Non-polymers1,0984
Water1,54986
1
A: Dihydrofolate reductase type 2
hetero molecules

A: Dihydrofolate reductase type 2
hetero molecules

A: Dihydrofolate reductase type 2
hetero molecules

A: Dihydrofolate reductase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,32220
Polymers26,9304
Non-polymers4,39216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area11300 Å2
ΔGint-43 kcal/mol
Surface area10680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.520, 67.520, 52.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit with the symmetry operations: x, y, z; y, x, -z; -x, -y, z; -y, -x, -z; The NADP ligand should be included only for the identity operator, and assigned full occupancy. Water molecules that clash with NADP should then be removed to obtain the set of waters that are valid for the tetramer. Tyr69 and Gln67 are also asymmetric, but the correlation of their alternate conformations to the asymmetric ligand binding has not been conclusively determined.

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Components

#1: Protein Dihydrofolate reductase type 2 / Dihydrofolate reductase type II


Mass: 6732.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
Strain: TMP-RESISTANT, CONTAINING R67 DHFR OVERPRODUCING PLASMID PLZ1
References: UniProt: P00383, dihydrofolate reductase
#2: 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
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50% 2-methyl-2,4-pentanediol (MPD), 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jul 30, 2007 / Details: Varimax HF, Confocal mirrors
RadiationMonochromator: Confocal mirrors (Varimax HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 4883 / Num. obs: 4883 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 13
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4.5 / Num. unique all: 396 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RH2

2rh2


Resolution: 1.9→22.86 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.928 / SU ML: 0.087 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Partial occupancies are estimates, and were not refined.
RfactorNum. reflection% reflectionSelection details
Rfree0.19991 257 5.3 %Random, preserved from 2RH2
Rwork0.14096 ---
obs0.14403 4623 97.95 %-
all-4880 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.783 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms441 0 68 86 595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021623
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2952.057875
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.559576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2742425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5131581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.382153
X-RAY DIFFRACTIONr_chiral_restr0.1670.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02499
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.25249
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.5416
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.31490
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.38268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.42633
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5621.5361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1852567
X-RAY DIFFRACTIONr_scbond_it2.9133325
X-RAY DIFFRACTIONr_scangle_it4.0324.5308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.933 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.342 7 -
Rwork0.187 185 -
obs--80 %

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