1W5P | pdb_00001w5p

Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C, D131C, D139C, P132E)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5SITTING DROP. DROPS WERE MIXED OF 3 MICROLITER OF PROTEIN SOLUTION (12 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 1MM ZNCL2, 10 MM DTT) PLUS 3 MICROLITER OF RESERVOIR SOLUTION (1M LITHIUM SULFATE, 100MM TRIS-HCL PH 8.5, 10MM NICKEL CHLORIDE), 100 MICROLITER OF RESERVOIR SOLUTION, 96 WELL PLATES (NUNC) IN AN ANAEROBIC BOX
Crystal Properties
Matthews coefficientSolvent content
2.346.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.97α = 90
b = 126.97β = 90
c = 86.432γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2003-11-04MSINGLE 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
11.5520990.081166.7101482
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)
11.551.61990.526.2

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 1B4K1.5591.2994390495096.70.1590.1570.170.1850.19RANDOM18.15
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]
-0.12-0.120.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.855
r_scangle_it2.768
r_mcangle_it2.064
r_scbond_it1.707
r_angle_refined_deg1.573
r_mcbond_it1.289
r_angle_other_deg0.831
r_symmetry_vdw_refined0.389
r_symmetry_vdw_other0.337
r_nbd_other0.254
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.855
r_scangle_it2.768
r_mcangle_it2.064
r_scbond_it1.707
r_angle_refined_deg1.573
r_mcbond_it1.289
r_angle_other_deg0.831
r_symmetry_vdw_refined0.389
r_symmetry_vdw_other0.337
r_nbd_other0.254
r_nbd_refined0.251
r_symmetry_hbond_refined0.144
r_chiral_restr0.108
r_xyhbond_nbd_refined0.106
r_nbtor_other0.084
r_bond_refined_d0.015
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms4992
Nucleic Acid Atoms
Solvent Atoms531
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing