3IU0

Structural basis for zymogen activation and substrate binding of transglutaminase from Streptomyces mobaraense

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	30% PEG8000, 50mM NaCl, 1mM EDTA, 1mM beta-mercaptoethanol, 0.01% NaN3, 100mM cacodylic acid, pH5.0 and 2% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.333	α = 90
b = 67.123	β = 90
c = 83.969	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	180					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	20	100	0.043	39.2	8.2		29327		-3	27.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.99	99.9		0.238	0.238	8.1	8	3592

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	PDB ENTRY 1IU4	1.9	19.129	26318	2953	99.99	0.213	0.21319	0.20971	0.24394	RANDOM	28.615

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]
0.015			0.004		-0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.947
r_dihedral_angle_4_deg	14.94
r_dihedral_angle_3_deg	14.278
r_dihedral_angle_1_deg	5.142
r_scangle_it	2.579
r_scbond_it	1.554
r_angle_refined_deg	1.056
r_mcangle_it	1.017
r_mcbond_it	0.542
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.947
r_dihedral_angle_4_deg	14.94
r_dihedral_angle_3_deg	14.278
r_dihedral_angle_1_deg	5.142
r_scangle_it	2.579
r_scbond_it	1.554
r_angle_refined_deg	1.056
r_mcangle_it	1.017
r_mcbond_it	0.542
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.189
r_nbd_refined	0.183
r_symmetry_hbond_refined	0.098
r_xyhbond_nbd_refined	0.094
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2777
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.