1L9N

Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions change structure for activation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L9M	PDB-ID 1L9M zymogen transglutaminase

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	294	4-12% (w/v) Peg 6K, 100 mM Bicine (pH 9) and 1% dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.488	α = 93.23
b = 116.537	β = 92.99
c = 60.768	γ = 89.51

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	ADSC QUANTUM 4	mirrors	2000-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	0.92	NSLS	X9B

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	2.1	20	97.9	14.9		80238	80238		-3	13.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	20	91.8

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB-ID 1L9M zymogen transglutaminase	2.1	20	78516	78516	7871		0.276	0.241	0.189	0.233	RANDOM	26

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]
-7.87	0.51	-4.48	-6.47	-0.92	14.34

RMS Deviations
Key	Refinement Restraint Deviation
o_dihedral_angle_d	25.44
c_angle_deg	1.28
c_improper_angle_d	0.73
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10500
Nucleic Acid Atoms
Solvent Atoms	1013
Heterogen Atoms	48

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

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.