4NEA | pdb_00004nea

1.90 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus in complex with NAD+ and BME-free Cys289

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MPB	PDB ENTRY 4MPB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	7 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, 2 mM NAD+, crystallization condition: JCSG+ Suite #G9 (0.1 M potassium thiocyonate, 30% w/v PEG2000 MME), VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.728	α = 90
b = 142.073	β = 90
c = 163.112	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	CCD	MARMOSAIC 300 mm CCD	beryllium lenses	2013-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.9	30	97.9	0.082	22.7	7.2	155760	155760		-3	24.4

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	1.9	1.93	100		0.446	4.6	7.2	7884

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	PDB ENTRY 4MPB	1.9	29.85	147576	147576	7781	97.85	0.14204	0.13965	0.15	0.188	0.2	RANDOM	26.568

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]
-0.33			1.27		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.951
r_dihedral_angle_4_deg	17.605
r_dihedral_angle_3_deg	14.349
r_dihedral_angle_1_deg	6.327
r_angle_refined_deg	1.698
r_angle_other_deg	0.85
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.951
r_dihedral_angle_4_deg	17.605
r_dihedral_angle_3_deg	14.349
r_dihedral_angle_1_deg	6.327
r_angle_refined_deg	1.698
r_angle_other_deg	0.85
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15543
Nucleic Acid Atoms
Solvent Atoms	1989
Heterogen Atoms	192

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.