9TDX | pdb_00009tdx

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

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	5.5	291	0.1M Bis-Tris, pH 5.5 and 2M ammonium sulfate using 2:1 ratio (protein:reservoir). Cryoprotected with 20% glycerol and flash-cooled in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.104	α = 90
b = 141.122	β = 90
c = 252.658	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		2025-05-14	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	49.408	99.9	0.129	0.055	0.999	16.1	12.5		189994

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	2.04	97.9		0.56	0.59	1.9	12.4

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	2.004	49.408	189881	9588	99.897	0.18	0.1792	0.1872	0.1977	0.2068	34.537

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]
1.487			-0.413		-1.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.21
r_dihedral_angle_3_deg	10.912
r_dihedral_angle_2_deg	8.996
r_dihedral_angle_1_deg	7.456
r_lrange_other	7.108
r_lrange_it	7.106
r_scangle_it	5.314
r_scangle_other	5.314
r_mcangle_it	4.19
r_mcangle_other	4.19
r_scbond_it	3.549
r_scbond_other	3.548
r_mcbond_it	2.938
r_mcbond_other	2.938
r_angle_refined_deg	1.38
r_angle_other_deg	0.526
r_symmetry_nbd_refined	0.354
r_nbd_other	0.297
r_symmetry_nbd_other	0.21
r_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.074
r_ncsr_local_group_6	0.051
r_ncsr_local_group_2	0.05
r_ncsr_local_group_5	0.05
r_ncsr_local_group_4	0.049
r_ncsr_local_group_1	0.044
r_ncsr_local_group_3	0.044
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16590
Nucleic Acid Atoms
Solvent Atoms	953
Heterogen Atoms	774

Software

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