3RCB | pdb_00003rcb

Crystal structure of the K102E mutant of KijD10, a 3-ketoreductase from Actinomadura kijaniata in complex with TDP-benzene and NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RBV	model generated using binary complex, PDB entry 3RBV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	1.2 M sodium/potassium phosphate, 100 mM HEPPS, 5 mM TDP-benzene, 5 mM NADP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.371	α = 90
b = 103.497	β = 90
c = 145.154	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	Bruker Platinum 135	montel mirrors	2011-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.49	84.27	96.9	0.096	0.096	10.6	4	18970	18970

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.58	86.9		0.238	0.238	3.2	10.6	1756

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 (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	model generated using binary complex, PDB entry 3RBV	2.49	65	18010	18010	959	97.04	0.19192	0.18883	0.19	0.25299	0.25	RANDOM	17.118

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]
-0.39			0.18		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.872
r_dihedral_angle_4_deg	20.421
r_dihedral_angle_3_deg	15.376
r_dihedral_angle_1_deg	6.79
r_scangle_it	5.637
r_scbond_it	3.755
r_angle_refined_deg	2.275
r_mcangle_it	2.13
r_mcbond_it	1.166
r_chiral_restr	0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.872
r_dihedral_angle_4_deg	20.421
r_dihedral_angle_3_deg	15.376
r_dihedral_angle_1_deg	6.79
r_scangle_it	5.637
r_scbond_it	3.755
r_angle_refined_deg	2.275
r_mcangle_it	2.13
r_mcbond_it	1.166
r_chiral_restr	0.135
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2478
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	117

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
SAINT	data reduction
SADABS	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.