3UAO | pdb_00003uao

Structure and Catalytic Mechanism of the Vitamin B3 Degradative Enzyme Maleamate Amidohydrolase from Bordetalla bronchiseptica RB50

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NBA	PDB ENTRY 1NBA MODIFIED TO TARGET SEQUENCE USING PHYRE SERVER

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	0.2 M ammonium acetate, 0.1 M sodium cacodylate, 30% PEG-8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.56	α = 90
b = 157.56	β = 90
c = 198.48	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	OXFORD RUBY CCD	mirrors	2010-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.399	12.01	91.7	0.087	9.78	2.2	143682	131825	3	3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.399	2.52	67.5		0.271		1.2	13186

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 1NBA MODIFIED TO TARGET SEQUENCE USING PHYRE SERVER	2.399	12.01	143682	131825	1368	97.94	0.12796	0.12704	0.13	0.17252	0.17	RANDOM	14.739

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]
-0.63			-0.63		1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.656
r_dihedral_angle_4_deg	16.457
r_dihedral_angle_3_deg	16.308
r_dihedral_angle_1_deg	10.077
r_scangle_it	3.047
r_scbond_it	1.891
r_angle_refined_deg	1.626
r_mcangle_it	1.136
r_angle_other_deg	1.133
r_mcbond_it	0.651
r_mcbond_other	0.137
r_chiral_restr	0.097
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11822
Nucleic Acid Atoms
Solvent Atoms	576
Heterogen Atoms	64

Software

Software
Software Name	Purpose
CrysalisPro	data collection
PHASER	phasing
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling