9TDW | pdb_00009tdw

Structure of D81A-Fructofuranosidase from Purpureocilum lilacinum in complex with fructose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	2M ammonium sulfate, 0.1M MES sodium salt pH 6.5, and 0.2M sodium chloride solution using 2:1 ratio (protein:reservoir). Cryoprotected with 20% glycerol and flash-cooled in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.175	α = 90
b = 141.777	β = 90
c = 253.741	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2024-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979257	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.4	48.805	99.7	0.153	0.063	0.998	18.2	13.3		112459

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44			0.463	0.748	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.4	48.805	112036	5644	99.682	0.201	0.1991	0.203	0.2286	0.2311	41.938

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]
-0.007			0.22		-0.212

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.705
r_dihedral_angle_3_deg	11.121
r_dihedral_angle_2_deg	8.013
r_lrange_other	7.905
r_lrange_it	7.902
r_dihedral_angle_1_deg	7.331
r_scangle_other	5.602
r_scangle_it	5.601
r_mcangle_it	5.319
r_mcangle_other	5.319
r_scbond_it	3.617
r_scbond_other	3.617
r_mcbond_it	3.494
r_mcbond_other	3.494
r_angle_refined_deg	1.315
r_angle_other_deg	0.499
r_symmetry_xyhbond_nbd_refined	0.29
r_nbd_other	0.272
r_symmetry_nbd_refined	0.252
r_symmetry_nbd_other	0.211
r_nbd_refined	0.185
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.128
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.085
r_chiral_restr	0.067
r_ncsr_local_group_1	0.053
r_ncsr_local_group_2	0.052
r_ncsr_local_group_5	0.052
r_ncsr_local_group_4	0.05
r_ncsr_local_group_3	0.048
r_ncsr_local_group_6	0.048
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16609
Nucleic Acid Atoms
Solvent Atoms	342
Heterogen Atoms	722

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing