PDB-2b6o: electron crystallographic structure of lens Aquaporin-0...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2b6o
Title	electron crystallographic structure of lens Aquaporin-0 (AQP0) (lens MIP) at 1.9A resolution, in a closed pore state
Descriptor	Lens fiber major intrinsic protein
Keywords	membrane protein, aquaporin-0 junctions, AQP0, lens MIP, lipid-protein interactions, membrane, lipid bilayer, closed water pore, electron crystallography
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Biological unit as octameric, Made by Jmol #2: Biological unit as octameric, Made by Jmol #3: Depositted structure unit, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	PDB-1sor PDB-1ymg PDB-2b6p
Similar strucutres (beta)	Diagram PDB-3b8k PDB-2brd PDB-2d57 PDB-3dww PDB-2zz9 List of similar structure data about Omokage system

Article
Citation - primary
Article	Nature, Vol. 438, Page: 633 - 638, Year: 2005,
Title	Lipid-protein interactions in double-layered two-dimensional AQP0 crystals.
Authors	Gonen, T., Cheng, Y., Sliz, P., Hiroaki, Y., Fujiyoshi, Y., Harrison, S.C., Walz, T.
Links	DOI: 10.1038/nature04321

Components
ID 1 : Aquaporin-0
Image
Description	Lens fiber major intrinsic protein
Type	polypeptide(L)
Formula weight	28285.104 Da
Number of molecules	1
ID	1
Source	Method: Isolated from a natural source Common name: sheep Genus: Ovis NCBI taxonomy: ID:9940 Organism scientific: Ovis aries
Links	UniProt: Q6J8I9, Sequence view
ID 2 : 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
Image
Description	1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
Type	non-polymer
Formula weight	677.940 Da
Number of molecules	9
ID	2
Source	Method: Obtained synthetically
ID 3 : water
Image
Description	water
Type	water
Formula weight	18.015 Da
Number of molecules	79
ID	3
Source	Method: Isolated from a natural source

Sample
Experiment
Method	ELECTRON CRYSTALLOGRAPHY
Crystals number	286
Crystal
Density Matthews	3.03
Density percent sol	59.44
Crystal grow
Method	MICRODIALYSIS
PH	6
Details	20mM MES pH 6.0, 50mM MgCl2, 5mM DTT, MICRODIALYSIS, temperature 300K
Temp	300 Kelvin

Processing
Reflection
Ordinal	1
B iso Wilson estimate	18.1
D resolution high	1.9
D resolution low	20
Rmerge I obs	0.166
Redundancy	5.7
Percent possible obs	80
Reflection shell
Ordinal	1
D res high	1.9
D res low	2.0
Redundancy	2.5
Percent possible all	70.5
2D projection selection
Software name	CNS 1.1
Computing
Data reduction ds	GATAN
Data reduction ii	GATAN
Structure refinement	CNS 1.1
Structure solution	CNS
Refine
Refine id	ELECTRON CRYSTALLOGRAPHY
B iso mean	58.4
Aniso B11	-7.32
Aniso B12	0.00
Aniso B13	0.00
Aniso B22	-7.32
Aniso B23	0.00
Aniso B33	14.64
Ls R factor R free	0.299
Ls R factor R free error	0.008
Ls R factor R work	0.258
Ls d res high	1.90 A
Ls d res low	5.00 A
Ls number reflection R free	1580
Ls number reflection all	16180
Ls number reflection obs	14600
Ls percent reflection R free	9.8
R Free selection details	RANDOM
Data cutoff high absF	2606056.45
Data cutoff low absF	0.000000
Isotropic thermal model	RESTRAINED
Ls cross valid method	THROUGHOUT
Ls sigma F	0.0
Method to determine struct	MOLECULAR REPLACEMENT
Starting model	1SOR - aquaporin-0 (MIP) strructure determined by electron crystallography PDB-1sor
Stereochemistry target values	Engh & Huber
Refine hist
Cycle id	LAST
Refine id	ELECTRON CRYSTALLOGRAPHY
D res high	1.90
D res low	5.00
Solvent atoms	79
Total atoms	2211
Ligand atoms	349
Protein atoms	1783
Software
Ordinal	1
Classification	data collection
Name	GATAN
Software
Ordinal	2
Classification	data reduction
Name	GATAN
Software
Ordinal	3
Classification	model building
Name	CNS
Software
Ordinal	4
Classification	refinement
Name	CNS
Version	1.1