2PWD | pdb_00002pwd

Crystal Structure of the Trehalulose Synthase MUTB from Pseudomonas Mesoacidophila MX-45 Complexed to the Inhibitor Deoxynojirmycin

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	290	13% PEG20000, 0.1M Na cacodylate, 0.01M L-cysteine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.4	α = 67.2
b = 72	β = 73.4
c = 82	γ = 70.9

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	2004-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.9330	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	42.3		0.086	9.72	2.1	110212	110212		1	9.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9			0.27	3.92	2.1	16151

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	FOURIER SYNTHESIS	THROUGHOUT	1ZJA	1.8	42.32	110211	5570	95.7	0.169	0.169	0.17	0.205	0.2	RANDOM	17.4

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]
0.32	-3.94	-1.21	2.32	2.54	-2.64

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.8
c_scangle_it	2.76
c_scbond_it	1.81
c_mcangle_it	1.64
c_angle_deg	1.4
c_mcbond_it	1.05
c_improper_angle_d	0.96
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8935
Nucleic Acid Atoms
Solvent Atoms	1515
Heterogen Atoms	24

Software

Software
Software Name	Purpose
CNS	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
CNS	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.