7D1E | pdb_00007d1e

Crystal structure of Bacteroides thetaiotaomicron glutaminyl cyclase bound to N-acetylhistamine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FUU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293.15	0.2 M NaCl, 0.1 M Bis-Tris, pH 5.5 and 25% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.308	α = 90
b = 77.381	β = 114.54
c = 48.867	γ = 90

Symmetry
Space Group	P 1 21 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	RAYONIX MX300HE		2018-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1.0	NSRRC	TPS 05A

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	1.85	45	100	0.117	10.8	3.6		23903

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	1.85	1.92	100		0.664	2.1	3.3

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	4FUU	1.85	44.45	22212	1195	97.69	0.1415	0.1388	0.15	0.1934	0.21	RANDOM	23.483

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]
-0.11		0.15	-0.33		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.86
r_sphericity_free	21.8
r_dihedral_angle_4_deg	19.339
r_dihedral_angle_3_deg	14.103
r_dihedral_angle_1_deg	5.821
r_sphericity_bonded	5.661
r_angle_refined_deg	1.41
r_rigid_bond_restr	1.374
r_angle_other_deg	0.948
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.86
r_sphericity_free	21.8
r_dihedral_angle_4_deg	19.339
r_dihedral_angle_3_deg	14.103
r_dihedral_angle_1_deg	5.821
r_sphericity_bonded	5.661
r_angle_refined_deg	1.41
r_rigid_bond_restr	1.374
r_angle_other_deg	0.948
r_chiral_restr	0.09
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2323
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	12

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.