2PRM

The structures of apo- and inhibitor bound human dihydroorotate dehydrogenase reveal conformational flexibility within the inhibitor binding site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D3G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.8293DROPS WERE FORMED BY MIXING EQUAL AMOUNTS OF 18-24 MG/ML PROTEIN IN 100 MM HEPES PH 7.0, 400 MM NACL, 30% GLYCEROL, 1 MM EDTA AND 10 MM N,N- DIMETHYLUNDECYLAMIN-N-OXIDE (C11DAO) WITH A PRECIPITANT SOLUTION OF 0.1 M ACETATE PH 4.8 40 MM C11DAO, 20.8 MM N, N-DIMETHYLDECYLAMINE-N-OXIDE (DDAO), 2 MM DIHYDROOROTATE (DHO) THE HANGING DROPS WERE INCUBATED AGAINST 0.5 ML RESERVOIR OF 0.1 M ACETATE PH 4.8, 1.6-2.2 M AMMONIUM SULFATE AND 30% GLYCEROL., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6265.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.05α = 90
b = 90.05β = 90
c = 123.2γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2004-04-27MSINGLE WAVELENGTH
21x-rayMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.092MAX III711

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,2319.599.50.256.8511941-318.753
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
341000.34656817

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1D3G319.5119385971000.1930.190.253RANDOM17.718
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.690.340.69-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.969
r_dihedral_angle_3_deg19.459
r_dihedral_angle_4_deg16.759
r_dihedral_angle_1_deg6.748
r_scangle_it3.533
r_scbond_it2.065
r_angle_refined_deg1.787
r_mcangle_it1.367
r_mcbond_it0.79
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.969
r_dihedral_angle_3_deg19.459
r_dihedral_angle_4_deg16.759
r_dihedral_angle_1_deg6.748
r_scangle_it3.533
r_scbond_it2.065
r_angle_refined_deg1.787
r_mcangle_it1.367
r_mcbond_it0.79
r_nbtor_refined0.319
r_symmetry_vdw_refined0.249
r_nbd_refined0.242
r_xyhbond_nbd_refined0.169
r_symmetry_hbond_refined0.166
r_chiral_restr0.113
r_bond_refined_d0.017
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2805
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms42

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
CNSphasing