1W56 | pdb_00001w56

Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C and D131C)


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. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (9 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM DTT) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (31.5 % (W/V) PEG 400, 100MM NA-HEPES PH 7.5, 20 MM MGCL2, 20MM BETA-MERCAPTOETHANOLE) ON GLASS COVER SLIDES,HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
2.2245.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.32α = 90
b = 126.32β = 90
c = 85.628γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2002-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW6MPG/DESY, HAMBURGBW6

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
11.72098.50.05217.84.375220
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)
11.71.76980.333.24.3

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-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1B4K1.787.7171529376898.50.140.1380.182RANDOM18.92
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]
0.150.15-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it7.696
r_dihedral_angle_1_deg6.145
r_scbond_it5.335
r_mcangle_it4.335
r_mcbond_it3.277
r_angle_refined_deg2.102
r_angle_other_deg1.017
r_symmetry_vdw_refined0.479
r_symmetry_vdw_other0.345
r_nbd_other0.259
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it7.696
r_dihedral_angle_1_deg6.145
r_scbond_it5.335
r_mcangle_it4.335
r_mcbond_it3.277
r_angle_refined_deg2.102
r_angle_other_deg1.017
r_symmetry_vdw_refined0.479
r_symmetry_vdw_other0.345
r_nbd_other0.259
r_nbd_refined0.223
r_symmetry_hbond_refined0.178
r_chiral_restr0.164
r_xyhbond_nbd_refined0.15
r_nbtor_other0.089
r_bond_refined_d0.025
r_gen_planes_refined0.009
r_gen_planes_other0.009
r_bond_other_d0.002
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 Atoms5051
Nucleic Acid Atoms
Solvent Atoms693
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing