2EBH | pdb_00002ebh

Crystal structures reveal a thiol-protease like catalytic triad in the C-terminal region of Pasteurella multocida toxin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EBF	PDB ENTRY 2EBF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	1.0M ammonium citrate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.755	α = 90
b = 150.559	β = 104.54
c = 77.91	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	MACSCIENCE	mirrors	2006-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	2.4	50	99.1	0.094		3.8	48566	47787

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)
	2.4	2.49	93.5		0.403		3.5	4466

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2EBF	2.4	43.69	0.403	47671	45259	2412	98.89	0.21471	0.213	0.21287	0.21	0.2494	0.25	RANDOM	43.807

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]
		0.01	-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.303
r_dihedral_angle_4_deg	18.603
r_dihedral_angle_3_deg	16.605
r_dihedral_angle_1_deg	5.26
r_scangle_it	1.486
r_angle_refined_deg	1.069
r_scbond_it	0.86
r_mcangle_it	0.851
r_mcbond_it	0.478
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.303
r_dihedral_angle_4_deg	18.603
r_dihedral_angle_3_deg	16.605
r_dihedral_angle_1_deg	5.26
r_scangle_it	1.486
r_angle_refined_deg	1.069
r_scbond_it	0.86
r_mcangle_it	0.851
r_mcbond_it	0.478
r_nbtor_refined	0.299
r_nbd_refined	0.185
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.13
r_symmetry_hbond_refined	0.119
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5643
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.