6V45 | pdb_00006v45

Crystal structure of a Probable carnitine operon oxidoreductase caia from Brucella melitensis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E5L	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental model	PDB	3ZGP	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental model	PDB	4A1K	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental model	PDB	4QRB	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental model	PDB	1ZAT	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental model	PDB	6NTW	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental model	PDB	4XVO	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental model	PDB	6D5A	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental model	PDB	4LZH	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A
experimental model	PDB	4Z7A	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	Optimization screen around condition Anatrace MCSG1_E6, well C4: 18.9% (w/V) PEG 3350, 200mM Potassium sulfate: BrmeA.18116.b.B2.PS01846 at 18.1mg/ml: tray 312854c4, cryo: 20% EG in 2 steps: puck xvm4-2.

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.06	α = 90
b = 96.06	β = 90
c = 96.06	γ = 90

Symmetry
Space Group	P 2 3

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	RAYONIX MX-300		2019-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.6	50	99.9	0.044	0.047	0.999	27.75	7.36		9354			71.381

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	100		0.639	0.687	0.862	3	7.511

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	MR-rosetta based on PDB entries 4LZH_A, 4A1K_A, 3ZGP_A, 6NTW_A, 5E5L_A, 1ZAT_A, 6D5A_A, 4XVO_B, 4QRB_A, 4Z7A_A	2.6	42.96	1.35	9352	934	99.96	0.2023	0.1986	0.2	0.2346	0.24	0	88.67

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	27.0533
f_angle_d	0.7077
f_chiral_restr	0.0517
f_bond_d	0.0048
f_plane_restr	0.0043

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1251
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	10

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	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.