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- PDB-2b6p: X-ray structure of lens Aquaporin-0 (AQP0) (lens MIP) in an open ... -

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Basic information

Entry
Database: PDB / ID: 2b6p
TitleX-ray structure of lens Aquaporin-0 (AQP0) (lens MIP) in an open pore state
ComponentsLens fiber major intrinsic protein
KeywordsMEMBRANE PROTEIN / aquaporin-0 / AQP0 / lens MIP / open water pore / aquaporin
Function / homology
Function and homology information


Passive transport by Aquaporins / gap junction-mediated intercellular transport / water channel activity / water transport / structural constituent of eye lens / gap junction / lens development in camera-type eye / positive regulation of cell adhesion / visual perception / protein homotetramerization ...Passive transport by Aquaporins / gap junction-mediated intercellular transport / water channel activity / water transport / structural constituent of eye lens / gap junction / lens development in camera-type eye / positive regulation of cell adhesion / visual perception / protein homotetramerization / calmodulin binding / apical plasma membrane / endoplasmic reticulum / plasma membrane
Similarity search - Function
Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Lens fiber major intrinsic protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGonen, T. / Cheng, Y. / Sliz, P. / Hiroaki, Y. / Fujiyoshi, Y. / Harrison, S.C. / Walz, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The Channel Architecture Of Aquaporin O At 2.2 Angstrom Resolution
Authors: Harries, W.E.C. / Akhavan, D. / Miercke, L.J.W. / Khademi, S. / Stroud, R.M.
History
DepositionOct 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 26, 2011Group: Other
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0THIS ENTRY 2B6P REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1YMGSF ORIGINAL DATA ...THIS ENTRY 2B6P REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1YMGSF ORIGINAL DATA DETERMINED BY AUTHOR: W.E.C.HARRIES,D.AKHAVAN,L.J.W.MIERCKE,S.KHADEMI, R.M.STROUD.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lens fiber major intrinsic protein


Theoretical massNumber of molelcules
Total (without water)28,2451
Polymers28,2451
Non-polymers00
Water2,324129
1
A: Lens fiber major intrinsic protein

A: Lens fiber major intrinsic protein

A: Lens fiber major intrinsic protein

A: Lens fiber major intrinsic protein


Theoretical massNumber of molelcules
Total (without water)112,9794
Polymers112,9794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area13830 Å2
ΔGint-125 kcal/mol
Surface area40440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.531, 109.531, 52.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Lens fiber major intrinsic protein / / Aquaporin-0 / MIP26 / MP26


Mass: 28244.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P06624
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.14 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1YMG.
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 20 mM glycine, pH 10.0 30% polyethylene glycol 1K 50 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→14.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 344976.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1218 10.1 %RANDOM
Rwork0.242 ---
all-0 --
obs-12037 92.6 %-
Displacement parametersBiso mean: 63.2 Å2
Baniso -1Baniso -2Baniso -3
1--11.45 Å20 Å20 Å2
2---11.45 Å20 Å2
3---22.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→14.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 0 129 2111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_deg1.3
X-RAY DIFFRACTIONo_dihedral_angle_d19.8
X-RAY DIFFRACTIONo_improper_angle_d0.9
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 185 10.5 %
Rwork0.265 1581 -
obs--84.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param

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