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- PDB-2b6o: Electron crystallographic structure of lens Aquaporin-0 (AQP0) (l... -

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Entry
Database: PDB / ID: 2b6o
TitleElectron crystallographic structure of lens Aquaporin-0 (AQP0) (lens MIP) at 1.9A resolution, in a closed pore state
DescriptorLens fiber major intrinsic protein
KeywordsMEMBRANE PROTEIN / aquaporin-0 junctions / AQP0 / lens MIP / lipid-protein interactions / membrane / lipid bilayer / closed water pore / membrane protein
Specimen sourceOvis aries / mammal / sheep / ヒツジ /
MethodElectron crystallography (1.9 Å resolution / 2d array / Crystallography / Molecular replacement)
AuthorsGonen, T. / Cheng, Y. / Sliz, P. / Hiroaki, Y. / Fujiyoshi, Y. / Harrison, S.C. / Walz, T.
CitationNature, 2005, 438, 633-638

Nature, 2005, 438, 633-638 StrPapers
Lipid-protein interactions in double-layered two-dimensional AQP0 crystals.
Tamir Gonen / Yifan Cheng / Piotr Sliz / Yoko Hiroaki / Yoshinori Fujiyoshi / Stephen C Harrison / Thomas Walz

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2005 / Release: Dec 6, 2005
RevisionDateData content typeGroupProviderType
1.0Dec 6, 2005Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance
Remark 240EXPERIMENT TYPE : ELECTRON DIFFRACTION DATE OF DATA COLLECTION : 01-DEC-2003 TEMPERATURE (KELVIN) : 300.0 PH : 6.00 NUMBER OF CRYSTALS USED : 286 RADIATION SOURCE : JEM3000SFF OPTICS : CRYSTALS TILTED TO MAX : 71.3 DEGREES DETECTOR TYPE : CCD DETECTOR MANUFACTURER : GATAN 2K X 2K DATA SCALING SOFTWARE : GATAN ACCELERATION VOLTAGE (KV) : 300 NUMBER OF UNIQUE REFLECTIONS : 22293 RESOLUTION RANGE HIGH (A) : 1.9 RESOLUTION RANGE LOW (A) : 20.000 OVERALL. COMPLETENESS FOR RANGE (%) : 80.0 DATA REDUNDANCY : 5.700 IN THE HIGHEST RESOLUTION SHELL. HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.0 COMPLETENESS FOR SHELL (%) : 82.0 DATA REDUNDANCY IN SHELL : 5.70 R MERGE FOR SHELL (I) : 0.166 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR : REPLACEMENT SOFTWARE USED: CNS STARTING MODEL: PDB ENTRY 1SOR

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Assembly

Deposited unit
A: Lens fiber major intrinsic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,38610
Polyers28,2851
Non-polymers6,1019
Water1,42379
#1
A: Lens fiber major intrinsic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)275,09080
Polyers226,2798
Non-polymers48,81172
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
#2
A: Lens fiber major intrinsic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)275,09080
Polyers226,2798
Non-polymers48,81172
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
crystal symmetry operation5_755-x+2,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area (Å2)82930
ΔGint (kcal/M)-755
Surface area (Å2)72410
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)65.500, 65.500, 160.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP 4 2 2

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Components

#1: Polypeptide(L)Lens fiber major intrinsic protein / Aquaporin-0


Mass: 28284.885 Da / Num. of mol.: 1 / Source: (natural) Ovis aries / mammal / ヒツジ / / References: UniProt: Q6J8I9

Cellular component

Molecular function

Biological process

#2: Chemical
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 9 / Formula: C36H72NO8P
#3: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 286
EM experimentAggregation state: 2D ARRAY / Reconstruction method: CRYSTALLOGRAPHY

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Sample preparation

ComponentName: aquaporin-0 / Type: COMPLEX
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM
EM embeddingDetails: 10% trehalose / Material: trehalose
VitrificationCryogen name: NITROGEN
CrystalDensity Matthews: 3.03 / Density percent sol: 59.44
Crystal growTemp: 300 K / Method: MICRODIALYSIS / pH: 6
Details: 20mM MES pH 6.0, 50mM MgCl2, 5mM DTT, MICRODIALYSIS, temperature 300K

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Data collection

MicroscopyMicroscope model: JEOL 3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: HELIUM / Specimen holder model: JEOL
Image recordingFilm or detector model: GENERIC GATAN (4k x 4k)
DiffractionMean temperature: 281 kelvins
SourceSource: ELECTRON MICROSCOPE / Type: JEM3000SFF
DetectorType: GATAN / Details: 4k X 4k / Detector: CCD / Collection date: Dec 1, 2003
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: electron
Radiation wavelengthRelative weight: 1
ReflectionB iso Wilson estimate: 18.1 Å2 / D resolution high: 1.9 Å / D resolution low: 20 Å / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.166 / Redundancy: 5.7 / Percent possible obs: 80
Reflection shellHighest resolution: 1.9 Å / Lowest resolution: 2 Å / Redundancy: 2.5 / Percent possible all: 70.5

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Processing

Software
NameClassification
GATANdata collection
GATANdata reduction
CNSrefinement
GATANdata scaling
CNSphasing
EM software
IDNameVersionCategory
1CNS1.1MODEL FITTING
2MRCRECONSTRUCTION
3D reconstructionSymmetry type: 2D CRYSTAL
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SOR - aquaporin-0 (MIP) strructure determined by electron crystallography
R Free selection details: RANDOM / Data cutoff high absF: 2606056.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Displacement parametersB iso mean: 58.4 Å2 / Aniso B11: -7.32 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -7.32 Å2 / Aniso B23: 0 Å2 / Aniso B33: 14.64 Å2
Least-squares processR factor R free: 0.299 / R factor R free error: 0.008 / R factor R work: 0.258 / Highest resolution: 1.9 Å / Lowest resolution: 5 Å / Number reflection R free: 1580 / Number reflection all: 16180 / Number reflection obs: 14600 / Percent reflection R free: 9.8
Refine analyzeLuzzati coordinate error free: 0.42 Å / Luzzati coordinate error obs: 0.37 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.65 Å / Luzzati sigma a obs: 0.63 Å
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 1783 / Nucleic acid: 0 / Ligand: 349 / Solvent: 79 / Total: 2211
Refine LS restraints
Refine IDTypeDev idealDev ideal target
ELECTRON CRYSTALLOGRAPHYo_bond_d0.016
ELECTRON CRYSTALLOGRAPHYo_angle_deg1.9
ELECTRON CRYSTALLOGRAPHYo_dihedral_angle_d19.8
ELECTRON CRYSTALLOGRAPHYo_improper_angle_d1.25
ELECTRON CRYSTALLOGRAPHYo_mcbond_it1.531.50
ELECTRON CRYSTALLOGRAPHYo_mcangle_it2.612.00
ELECTRON CRYSTALLOGRAPHYo_scbond_it1.632.00
ELECTRON CRYSTALLOGRAPHYo_scangle_it2.442.50
Xplor file
Refine IDSerial noParam fileTopol file
ELECTRON CRYSTALLOGRAPHY1protein_rep.paramprotein.top
ELECTRON CRYSTALLOGRAPHY2water_rep.paramwater.top
ELECTRON CRYSTALLOGRAPHY3dmpc.paramdmpc_all_final.top

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