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- PDB-2c32: Co-axial association of recombinant eye lens aquaporin-0 observed... -

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Basic information

Entry
Database: PDB / ID: 2c32
TitleCo-axial association of recombinant eye lens aquaporin-0 observed in loosely packed 3D-crystals
ComponentsLENS FIBER MAJOR INTRINSIC PROTEIN
KeywordsMEMBRANE PROTEIN / EYE LENS / MIXED MICELLE / GAP JUNCTION / PHOSPHORYLATION / TRANSMEMBRANE
Function / homology
Function and homology information


Passive transport by Aquaporins / gap junction-mediated intercellular transport / water transport / water channel activity / 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 transport / water channel activity / 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
Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
Lens fiber major intrinsic protein
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.01 Å
AuthorsPalanivelu, D.V. / Schirmer, T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Co-Axial Association of Recombinant Eye Lens Aquaporin-0 Observed in Loosely Packed 3D-Crystals
Authors: Palanivelu, D.V. / Kozono, D.E. / Engel, A. / Suda, K. / Lustig, A. / Agre, P. / Schirmer, T.
History
DepositionOct 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
Water00
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)188.271, 188.271, 188.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein LENS FIBER MAJOR INTRINSIC PROTEIN / AQUAPORIN-0 / AQP0 / MIP26 / MP26


Mass: 28244.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Organ: EYE / Plasmid: PYES2.0 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): SC334 / References: UniProt: P06624

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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: 5.32 Å3/Da / Density % sol: 76.8 %
Crystal growpH: 8.9
Details: 100 MM BICINE NAOH PH 8.9, 350 MM NACL, 34 % (V/V) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9797
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 7.01→15 Å / Num. obs: 900 / % possible obs: 89.9 % / Observed criterion σ(I): 0 / Redundancy: 6.69 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.21
Reflection shellResolution: 7.01→7.38 Å / Redundancy: 6.96 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.06 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YMG

1ymg


Resolution: 7.01→15 Å / Cor.coef. Fo:Fc: 0.756 / Cor.coef. Fo:Fc free: 0.781 / SU B: 517.315 / SU ML: 3.822 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 4.233 / ESU R Free: 4.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE SOLVED BY MOLECULAR REPLACEMENT AND RIGID BODY REFINEMENT (1 BODY, I.E. THE MONOMER OF THE CRYSTALLOGRAPHIC TETRAMER)
RfactorNum. reflection% reflectionSelection details
Rfree0.387 102 11.333 %RANDOM
Rwork0.39 ---
obs0.39 900 99.6 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.75 Å2
Refinement stepCycle: LAST / Resolution: 7.01→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 0 0 1761
LS refinement shellResolution: 7.01→7.3 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.636 11
Rwork0.45 103

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