4FJ0 | pdb_00004fj0

Crystal structure of the ternary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Holo form) and 3,7-dihydroxy flavone

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QWI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	30% (W/V) PEG 2000 MME, 0.1M KCNS, 5 mM NADP. Crystals soaked for 24 hours in: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 15% (V/V)ETHYLENE GLYCOLE, 5% (V/V) DMSO, 1 mM NADP, 0.8 mM 3,7-dihydroxyflavone, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.34	α = 90
b = 113.25	β = 102.76
c = 69.31	γ = 90

Symmetry
Space Group	P 1 21 1

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 2M	Platinum coated cylindrical mirror	2010-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.2	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	45	95.1	0.079	11.8	3.5	45372	45372		-3	35

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.33	82.4		0.267	3.71	2.65	6010

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3QWI	2.2	43.41	43102	43102	2269	95.2	0.17173	0.17173	0.16997	0.1761	0.20469	0.2101	RANDOM	24.731

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]
-0.67		-1.71	1.25		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.952
r_dihedral_angle_3_deg	13.676
r_dihedral_angle_4_deg	8.852
r_dihedral_angle_1_deg	5.689
r_angle_refined_deg	1.389
r_angle_other_deg	1.208
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.952
r_dihedral_angle_3_deg	13.676
r_dihedral_angle_4_deg	8.852
r_dihedral_angle_1_deg	5.689
r_angle_refined_deg	1.389
r_angle_other_deg	1.208
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7851
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	262

Software

Software
Software Name	Purpose
XRD1	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.