6ULW | pdb_00006ulw

Adenylation, ketoreductase, and pseudo Asub multidomain structure of a keto acid-selecting NRPS module

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R0M	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	4IZ6	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	4DG8	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	3TSY	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	3KXW	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	3G7S	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	3ETC	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	2VSQ	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	5D2E	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	4L4X	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	4J1Q	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	4IMP	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	4HXY	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	3SLK	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	3QP9	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	3MJT	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	2Z5L	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1
experimental model	PDB	2FR1	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.165 M sodium succinate, 0.24 % v/v PEG2000 MME, 0.02 M HEPES, 0.016 M sodium chloride, 5.9% v/v PEG3350, 0.104 M calcium acetate, 0.01 M phenol

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.66	α = 90
b = 143.66	β = 90
c = 431.87	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 EIGER X 16M		2017-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.979200	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	3.4	100	98	0.123	0.999	8.86	3.5		121921			141.68

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.49	87		0.136	0.33	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entries 4R0M, 4IZ6, 4DG8, 3TSY, 3KXW, 3G7S, 3ETC, 2VSQ, 5D2E, 4L4X, 4J1Q, 4IMP, 4HXY, 3SLK, 3QP9, 3MJT, 2Z5L, & 2FR1	3.4	49.11	1.35	120166	5958	98.61	0.2299	0.2276	0.275	181.88

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
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.7413
f_angle_d	0.6798
f_chiral_restr	0.0441
f_plane_restr	0.0043
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	37831
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	9

Software

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

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.