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- PDB-1ymg: The Channel Architecture of Aquaporin O at 2.2 Angstrom Resolution -

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Basic information

Entry
Database: PDB / ID: 1ymg
TitleThe Channel Architecture of Aquaporin O at 2.2 Angstrom Resolution
ComponentsLens fiber major intrinsic protein
KeywordsMEMBRANE PROTEIN / AQP0 / Integral Membrane Protein / MIP26 / Lens / Cataract / Water Channel
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsHarries, W.E.C. / Akhavan, D. / Miercke, L.J.W. / Khademi, S. / Stroud, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The Channel Architecture of Aquaporin 0 at a 2.2-A Resolution
Authors: Harries, W.E.C. / Akhavan, D. / Miercke, L.J.W. / Khademi, S. / Stroud, R.M.
History
DepositionJan 20, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 8, 2005ID: 1TM8
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 9, 2012Group: Structure summary
Revision 1.4Jun 20, 2012Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.occupancy / _chem_comp.mon_nstd_flag ..._atom_site.occupancy / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lens fiber major intrinsic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8583
Polymers28,2451
Non-polymers6132
Water3,279182
1
A: Lens fiber major intrinsic protein
hetero molecules

A: Lens fiber major intrinsic protein
hetero molecules

A: Lens fiber major intrinsic protein
hetero molecules

A: Lens fiber major intrinsic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,43112
Polymers112,9794
Non-polymers2,4518
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 area17800 Å2
ΔGint-105 kcal/mol
Surface area30250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.531, 110.531, 53.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-524-

HOH

21A-579-

HOH

DetailsThe monomers arrange into a tetramer generated from the monomer by the operations: -x,-y,z: 1/2-y, 1/2: 1/2+y,1/2

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Components

#1: Protein Lens fiber major intrinsic protein / / MIP26 / MP26 / AQP0


Mass: 28244.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ocular lens fiber cell plasma membrane / Source: (natural) Bos taurus (cattle) / Cell: FIBER / Cellular location: PLASMA MEMBRANECell membrane / Organ: EYE / Tissue: LENS / References: UniProt: P06624
#2: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 30% polyethylene glycol 1000, 20 mM glycine, 50 mM NaCl, pH 10.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2003
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
21.115871
ReflectionResolution: 2.2→30 Å / Num. all: 16385 / Num. obs: 16284 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 20.3 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 27.96
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.5 / % possible all: 80

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J4N

1j4n


Resolution: 2.24→25.26 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 328368.91 / 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
Rfree0.303 1468 10 %RANDOM
Rwork0.24 ---
all0.246 16284 --
obs0.24 14682 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 93.2556 Å2 / ksol: 0.327246 e/Å3
Displacement parametersBiso mean: 53.1 Å2
Baniso -1Baniso -2Baniso -3
1--11.66 Å20 Å20 Å2
2---11.66 Å20 Å2
3---23.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.24→25.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 42 182 1985
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.272.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.449 117 8.4 %
Rwork0.379 1272 -
obs--49.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3BNG.PARAMBNG.TOP

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