1QOQ

CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH INDOLE GLYCEROL PHOSPHATE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QOPPDB ENTRY 1QOP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8ENZYME SOLUTION: 10 MG/ML TRPS IN 50 MM BICINE PH 7.8, 1 MM EDTA, 5 MM DITHIOERYTHRITOL, 20 MUM PYRIDOXAL-5'-PHOSPHATE, RESERVOIR SOLUTION: 50 MM BICINE PH 7.8, 5 MM EDTA, 5 MM DITHIOERYTHRITOL, 0.1 MM PYRIDOXAL-5'-PHOSPHATE, 2 MM SPERMINE, 8-12 % PEG 8000, HANGING DROP GEOMETRY IN CONTRAST TO WHAT HAS BEEN IMPLICATED IN THE PUBLICATION ASSOCIATED WITH THIS PDB-ENTRY (WEYAND & SCHLICHTING, BIOCHEMISTRY 38: 16469-16480, (1999)), THE PH OF THE COMPLEX WAS NOT NEUTRAL BUT 5.0-5.2. THEREFORE, THE STRUCTURE WAS RE-DETERMINED AT PH 7.0 (PDB CODE 2RHG) AND ALSO AT PH 9.0 (PDB CODE 2RH9). THIS DATA SHOWS THAT CLOSURE OF LOOP ALPHA-L6 IS CAUSED BY THE LOW PH AND NOT BY BINDING OF IGP
Crystal Properties
Matthews coefficientSolvent content
2.5752.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.742α = 90
b = 60.055β = 94.48
c = 67.098γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD1998-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12CNSLSX12C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.831.294.50.07611.73.4963674-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.970.80.212.61.57

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QOP1.820636503126940.1710.21RANDOM21.1
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor28.2
p_special_tor15
p_staggered_tor13.4
p_planar_tor4.1
p_scangle_it3.351
p_scbond_it2.215
p_mcangle_it2.128
p_mcbond_it1.537
p_xhyhbond_nbd0.3
p_multtor_nbd0.259
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor28.2
p_special_tor15
p_staggered_tor13.4
p_planar_tor4.1
p_scangle_it3.351
p_scbond_it2.215
p_mcangle_it2.128
p_mcbond_it1.537
p_xhyhbond_nbd0.3
p_multtor_nbd0.259
p_singtor_nbd0.175
p_chiral_restr0.154
p_xyhbond_nbd0.11
p_planar_d0.038
p_angle_d0.033
p_plane_restr0.0254
p_bond_d0.017
p_angle_deg
p_hb_or_metal_coord
p_orthonormal_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4898
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing