2PZN | pdb_00002pzn

The crystallographic structure of Aldose Reductase IDD393 complex confirms Leu300 as a specificity determinant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T41	ALDOSE REDUCTASE COMPLEXED WITH IDDD552 (PDB ID: 1T41)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	Protein was co-crystallized with NADP+ (Sigma) and inhibitor (ratios protein/coenzyme/inhibitor = 1/2/2). Previously equilibrated (ammonium citrate buffer, PEG 6000 (15%)) hanging drops were seeded with stock seed solutions diluted 100 times. Cryofreezing was carried out through quick transfers into a stabilization solution (25% PEG 6000), then into a cryo-protecting solution (40% PEG 6000) and finally into either liquid nitrogen or ethane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.224	α = 67.58
b = 47.154	β = 76.47
c = 40.316	γ = 76.11

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	SBC-2	1.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION HARMONIC CONTAMINATION	1999-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.90042	APS	19-ID

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	50	94.91	0.062	13.65		167901	158045

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	1.04	85.6		0.271	3.6

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	ALDOSE REDUCTASE COMPLEXED WITH IDDD552 (PDB ID: 1T41)	1	10	158045	149983		90.2	0.1286		0.13		0.15	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
110	2439.16	2996.72

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.113
s_non_zero_chiral_vol	0.101
s_zero_chiral_vol	0.096
s_similar_adp_cmpnt	0.049
s_anti_bump_dis_restr	0.036
s_angle_d	0.033
s_from_restr_planes	0.0296
s_bond_d	0.014
s_rigid_bond_adp_cmpnt	0.005
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2936
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	73

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
Propietary	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	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.