1Q51

Crystal Structure of Mycobacterium tuberculosis MenB in Complex with Acetoacetyl-Coenzyme A, a Key Enzyme in Vitamin K2 Biosynthesis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DUB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	dioxane, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.401	α = 90
b = 139.389	β = 97.31
c = 142.041	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	CCD	ADSC QUANTUM 4		2002-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.1	NSLS	X26C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	50					146353

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1DUB	2.3	50	146353	7777	99.62	0.20369	0.20369	0.20171	0.24106	RANDOM	34.919

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]
4.24		0.1	-1.59		-2.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.394
r_scangle_it	2.895
r_scbond_it	1.831
r_angle_refined_deg	1.495
r_mcangle_it	1.231
r_mcbond_it	0.639
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.394
r_scangle_it	2.895
r_scbond_it	1.831
r_angle_refined_deg	1.495
r_mcangle_it	1.231
r_mcbond_it	0.639
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.107
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25697
Nucleic Acid Atoms
Solvent Atoms	422
Heterogen Atoms	648

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	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.