2VK1

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant D28A in complex with its substrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QPBPDB ENTRY 1QPB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.3527315MM CITRATE, 1,67MM MES, 315MM PYRUVATE, 1MM NADH, 0.001MG/ML ALCOHOL DEHYDROGENASE, 1.67MM TDP, 1.67MM MAGNESIUM SULFATE, 1.67MM DTT, 11.25% PEG 2000, 11.25% PEG 6000, 1.1MG SCPDC/ML PH 6.35, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273.15C
Crystal Properties
Matthews coefficientSolvent content
2.5451.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.88α = 90
b = 141.31β = 107.19
c = 114.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.719999.30.0717.53.62621511
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)
11.711.7499.20.572.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1QPB1.71109.11260330131399.10.1910.1910.22RANDOM20.91
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]
-0.09-0.320.78-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.855
r_dihedral_angle_4_deg19.513
r_dihedral_angle_3_deg14.173
r_dihedral_angle_1_deg5.714
r_scangle_it3.295
r_scbond_it2.193
r_angle_refined_deg1.45
r_mcangle_it1.307
r_mcbond_it0.755
r_chiral_restr0.514
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.855
r_dihedral_angle_4_deg19.513
r_dihedral_angle_3_deg14.173
r_dihedral_angle_1_deg5.714
r_scangle_it3.295
r_scbond_it2.193
r_angle_refined_deg1.45
r_mcangle_it1.307
r_mcbond_it0.755
r_chiral_restr0.514
r_nbtor_refined0.309
r_nbd_refined0.219
r_symmetry_vdw_refined0.2
r_xyhbond_nbd_refined0.125
r_symmetry_hbond_refined0.123
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17280
Nucleic Acid Atoms
Solvent Atoms1558
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing