6ULW

Adenylation, ketoreductase, and pseudo Asub multidomain structure of a keto acid-selecting NRPS module


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4R0MPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 4IZ6PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 4DG8PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 3TSYPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 3KXWPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 3G7SPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 3ETCPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 2VSQPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 5D2EPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 4L4XPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 4J1QPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 4IMPPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 4HXYPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 3SLKPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 3QP9PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 3MJTPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 2Z5LPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental modelPDB 2FR1PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.165 M sodium succinate, 0.24 % v/v PEG2000 MME, 0.02 M HEPES, 0.016 M sodium chloride, 5.9% v/v PEG3350, 0.104 M calcium acetate, 0.01 M phenol
Crystal Properties
Matthews coefficientSolvent content
3.6966.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.66α = 90
b = 143.66β = 90
c = 431.87γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979200APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
13.4100980.1230.9998.863.5121921141.68
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.43.49870.1360.332.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR13.449.111.35120166595898.610.22990.22760.275181.88
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
f_dihedral_angle_d20.7413
f_angle_d0.6798
f_chiral_restr0.0441
f_plane_restr0.0043
f_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms37831
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms9

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing