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- PDB-4p3r: Cryogenic WT DHFR, time-averaged ensemble -

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Basic information

Entry
Database: PDB / ID: 4p3r
TitleCryogenic WT DHFR, time-averaged ensemble
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD
Function / homologyDihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsKeedy, D.A. / van den Bedem, H. / Fraser, J.S.
CitationJournal: Structure / Year: 2014
Title: Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR.
Authors: Keedy, D.A. / van den Bedem, H. / Sivak, D.A. / Petsko, G.A. / Ringe, D. / Wilson, M.A. / Fraser, J.S.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Jul 27, 2016Group: Data collection
Revision 1.4Aug 10, 2016Group: Data collection
Revision 1.5Nov 22, 2017Group: Derived calculations / Refinement description / Structure summary
Category: entity / pdbx_struct_oper_list / software
Item: _entity.pdbx_number_of_molecules / _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)19,2043
Polymers18,0191
Non-polymers1,1852
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.04, 44.82, 98.2
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Number of models250

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Components

#1: Protein Dihydrofolate reductase


Mass: 18019.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / DH10B / Gene: folA, ECDH10B_0049 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XC49, dihydrofolate reductase
#2: Chemical ChemComp-FOL / FOLIC ACID


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


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100MM HEPES PH 7.5, 21% PEG8000, 200MM MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2011
RadiationMonochromator: KOHZU DUAL DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 51212 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Net I/σ(I): 22.6
Reflection shellResolution: 1.15→1.19 Å / % possible all: 64.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.ensemble_refinement: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→40.774 Å / SU ML: 0.04 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.37
RfactorNum. reflection% reflection
Rfree0.1362 2598 5.07 %
Rwork0.1093 --
obs0.1107 51212 94.42 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→40.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 80 200 1548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.017
X-RAY DIFFRACTIONf_angle_d4.34
X-RAY DIFFRACTIONf_dihedral_angle_d17.46
X-RAY DIFFRACTIONf_chiral_restr0.118
X-RAY DIFFRACTIONf_plane_restr0.012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1503-1.17120.2047880.13611553X-RAY DIFFRACTION58
1.1712-1.19370.16551040.1291895X-RAY DIFFRACTION72
1.1937-1.21810.16491220.12632116X-RAY DIFFRACTION79
1.2181-1.24460.15951290.12522354X-RAY DIFFRACTION88
1.2446-1.27360.15431430.11132590X-RAY DIFFRACTION97
1.2736-1.30540.13841360.10352671X-RAY DIFFRACTION100
1.3054-1.34070.13941520.09982656X-RAY DIFFRACTION100
1.3407-1.38020.15351400.10022674X-RAY DIFFRACTION100
1.3802-1.42470.13851220.09632704X-RAY DIFFRACTION100
1.4247-1.47560.12031380.09442704X-RAY DIFFRACTION100
1.4756-1.53470.11491540.09492653X-RAY DIFFRACTION100
1.5347-1.60460.13291320.09112719X-RAY DIFFRACTION100
1.6046-1.68920.11061450.09132694X-RAY DIFFRACTION100
1.6892-1.7950.1191410.09292738X-RAY DIFFRACTION100
1.795-1.93360.1131200.09722736X-RAY DIFFRACTION100
1.9336-2.12820.13081590.10262732X-RAY DIFFRACTION100
2.1282-2.43610.11831530.10862736X-RAY DIFFRACTION100
2.4361-3.06910.14911590.11532766X-RAY DIFFRACTION100
3.0691-40.79950.14741610.13232923X-RAY DIFFRACTION100

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