6TKX | pdb_00006tkx

Carbohydrate esterase from gut microbiota


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HXK3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 4N5H3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 5AO93HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 2WTM3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 3BXP3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 3BJR3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 4V2I3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 2C7B3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 4E153HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 4Q3K3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 3PFB3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 3ZWQ3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 5L2P3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 3QH43HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 5G5C3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 5JD43HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 4ZI53HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 3F673HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 5CML3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8
experimental modelPDB 4WY83HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.2 M Ammonium sulfate, 25% PEG MME 5000, 0.1 M mes pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.141.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.46α = 90
b = 108.46β = 90
c = 44.79γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
12.0641.39999.90.1430.6108.717093
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.062.11.50.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY82.0641.3991.351705583299.850.20860.20540.210.27020.27
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_d12.58
f_angle_d1.156
f_chiral_restr0.058
f_bond_d0.012
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2212
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms5

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
Rosettaphasing