1W54 | pdb_00001w54

Stepwise introduction of a zinc binding site into Porphobilinogen synthase from Pseudomonas aeruginosa (mutation D139C)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B4KPDB ENTRY 1B4K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (8,7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10 MM MGCL2, 10 ZNCL2, 10 MM DTT) PLUS 5 MICROL RESERVOIR SOLUTION (28,5 % (W/V) PEG-400, 100 MM NA-HEPES PH 7.5, 80MM MGCL2, 20MM DTT) ABOVE 500 MICROL OF RESERVOIR SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
2.2344.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.231α = 90
b = 125.232β = 90
c = 86.03γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU R-AXIS IVBLUE OPTIC2002-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
12.247.199.80.123.112.635228
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)
12.22.2899.50.455.311.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1B4K2.287.7133396181199.70.1570.1540.160.2170.22RANDOM30.84
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]
0.570.57-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.203
r_dihedral_angle_1_deg5.359
r_mcangle_it4.869
r_scbond_it4.199
r_mcbond_it3.553
r_angle_refined_deg1.928
r_angle_other_deg1.166
r_symmetry_vdw_other0.31
r_symmetry_vdw_refined0.265
r_nbd_other0.231
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.203
r_dihedral_angle_1_deg5.359
r_mcangle_it4.869
r_scbond_it4.199
r_mcbond_it3.553
r_angle_refined_deg1.928
r_angle_other_deg1.166
r_symmetry_vdw_other0.31
r_symmetry_vdw_refined0.265
r_nbd_other0.231
r_nbd_refined0.217
r_chiral_restr0.151
r_symmetry_hbond_refined0.132
r_xyhbond_nbd_refined0.128
r_nbtor_other0.084
r_bond_refined_d0.026
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.005
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms4899
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing