2I7B | pdb_00002i7b

Structure of the naturally occuring mutant of human ABO(H) Blood group B glycosyltransferase: GTB/A268T

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LZ7	PDB ENTRY 1LZ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				6-8 mg/ml GTB/A268T, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA), pH 7.5, 50 mM CH3COONa, pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (w/v) 2-methyl-2,4-pentanediol (MPD), 5% (w/v) glycerol, 2% (w/v) PEG 4000 and 0.3-0.5 mM

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.54	α = 90
b = 148.95	β = 90
c = 80	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	IMAGE PLATE	RIGAKU RAXIS IV	Osmic "Blue" Confocal x-ray mirrors (Osmic)	2006-05-27	M	SINGLE WAVELENGTH

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

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	1.99	20	96.9	0.06	12.9	4.86	21947	21267

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	1.99	2.06	99.4		0.296	4.2	4.6	2128

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 (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 1LZ7	1.99	20	20163	1102	96.85	0.18713	0.1847	0.18	0.23063	0.23	RANDOM	31.973

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]
-0.8			0.61		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.768
r_dihedral_angle_4_deg	18.183
r_dihedral_angle_3_deg	14.353
r_dihedral_angle_1_deg	6.642
r_scangle_it	4.085
r_scbond_it	2.774
r_mcangle_it	1.806
r_angle_refined_deg	1.697
r_mcbond_it	1.213
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.768
r_dihedral_angle_4_deg	18.183
r_dihedral_angle_3_deg	14.353
r_dihedral_angle_1_deg	6.642
r_scangle_it	4.085
r_scbond_it	2.774
r_mcangle_it	1.806
r_angle_refined_deg	1.697
r_mcbond_it	1.213
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.126
r_bond_refined_d	0.022
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2143
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	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.