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- PDB-4m7u: Dihydrofolate reductase from Enterococcus faecalis complexed with... -

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Basic information

Entry
Database: PDB / ID: 4m7u
TitleDihydrofolate reductase from Enterococcus faecalis complexed with NADP(H)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / reduction of dihydrofolate to tetrahydrofolate
Function / homology
Function and homology information


dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / 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 (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1014 Å
AuthorsBourne, C.R.
CitationJournal: Biochemistry / Year: 2014
Title: The Structure and Competitive Substrate Inhibition of Dihydrofolate Reductase from Enterococcus faecalis Reveal Restrictions to Cofactor Docking.
Authors: Bourne, C.R. / Wakeham, N. / Webb, N. / Nammalwar, B. / Bunce, R.A. / Berlin, K.D. / Barrow, W.W.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7892
Polymers20,0461
Non-polymers7431
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.254, 63.254, 97.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

#1: Protein Dihydrofolate reductase


Mass: 20045.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal Strep tag with cleaved thrombin site; uncleaved N-terminal TEV site
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: 700802 / Gene: dihydrofolate reductase, EF_1577, folA / Plasmid: pPSG-IBA3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q834R2, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: polyethylene glycol 3350, 1.5 M ammonium citrate dibasic pH 7 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.101→40.63 Å / Num. all: 12062 / Num. obs: 11841 / % possible obs: 98.17 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.097 / Net I/σ(I): 9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS-MODEL homology model based on 1ZDR

1zdr


Resolution: 2.1014→40.628 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 589 5.02 %5% random selection
Rwork0.1835 ---
obs0.1855 11737 97.32 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1014→40.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 48 131 1541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081504
X-RAY DIFFRACTIONf_angle_d1.2292065
X-RAY DIFFRACTIONf_dihedral_angle_d29.428624
X-RAY DIFFRACTIONf_chiral_restr0.108227
X-RAY DIFFRACTIONf_plane_restr0.008249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1014-2.31280.28181430.21572642X-RAY DIFFRACTION95
2.3128-2.64750.26471450.20512783X-RAY DIFFRACTION99
2.6475-3.33530.24591480.19142818X-RAY DIFFRACTION99
3.3353-40.63580.18211530.16312905X-RAY DIFFRACTION97

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