5D9P | pdb_00005d9p

Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella bryantii B14, in complex with an inhibitory N-bromoacetylglycosylamine derivative of XXXG

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VDH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	28 mg/mL plus 6.6 mM EDTA, incubated 4 degrees overnight, then added 8M XXXG-NHCOCH2Br (inhibitor), incubated at 37 degrees for 3 h, then 0.5 microL of this solution was mixed with 0.5 microL of reservoir solution: 0.2 M calcium chloride, 20% (w/v) PEG3350. Cryoprotectant = paratone-N oil.

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.192	α = 76.39
b = 49.015	β = 89.98
c = 85.972	γ = 66.8

Symmetry
Space Group	P 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	RIGAKU SATURN A200		2014-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	1.8	31.921	92.8	0.06	11.47	1.9		60113

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	1.8	1.85	86.5		0.309	2.13	1.7

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3VDH	1.8	31.921	1.96	60096	1850	92.7	0.1646	0.1633	0.17	0.2041	0.21	Random selection

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	12.508
f_angle_d	1.189
f_chiral_restr	0.046
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5444
Nucleic Acid Atoms
Solvent Atoms	750
Heterogen Atoms	302

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
Coot	model building

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.