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- PDB-5i32: Ammonia permeable aquaporin AtTIP2;1 -

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Basic information

Entry
Database: PDB / ID: 5i32
TitleAmmonia permeable aquaporin AtTIP2;1
ComponentsAquaporin TIP2-1
KeywordsMEMBRANE PROTEIN / Aquaporin / MIP / ammonia-permeable
Function / homology
Function and homology information


central vacuole / methylammonium transmembrane transporter activity / protein storage vacuole / plant-type vacuole membrane / plant-type cell wall / water channel activity / water transport / plasmodesma / chloroplast envelope / cell wall ...central vacuole / methylammonium transmembrane transporter activity / protein storage vacuole / plant-type vacuole membrane / plant-type cell wall / water channel activity / water transport / plasmodesma / chloroplast envelope / cell wall / vacuole / vacuolar membrane / membrane => GO:0016020 / Golgi apparatus / identical protein binding / 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
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.18 Å
AuthorsKirscht, A. / Nissen, P. / Kjellbom, P. / Gourdon, P. / Johanson, U.
Funding support Sweden, Denmark, 6items
OrganizationGrant numberCountry
Swedish Research Council Sweden
(Biomemos) of the European Research Council
Danscatt program of the Danish Council of Independent Research Denmark
BioStruct-X860
Formas, the Research School of Pharmaceutical Sciences FLAEK Sweden
CitationJournal: Plos Biol. / Year: 2016
Title: Crystal Structure of an Ammonia-Permeable Aquaporin.
Authors: Kirscht, A. / Kaptan, S.S. / Bienert, G.P. / Chaumont, F. / Nissen, P. / de Groot, B.L. / Kjellbom, P. / Gourdon, P. / Johanson, U.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aquaporin TIP2-1


Theoretical massNumber of molelcules
Total (without water)28,0431
Polymers28,0431
Non-polymers00
Water2,360131
1
A: Aquaporin TIP2-1

A: Aquaporin TIP2-1

A: Aquaporin TIP2-1

A: Aquaporin TIP2-1


Theoretical massNumber of molelcules
Total (without water)112,1724
Polymers112,1724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area13890 Å2
ΔGint-161 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.270, 89.270, 82.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Aquaporin TIP2-1 / Delta-tonoplast intrinsic protein / Delta-TIP / Tonoplast intrinsic protein 2-1 / AtTIP2 / 1


Mass: 28043.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal deca-His-tag_Spacer_Tev-cleavage-site Start-Met is exchanged to Gly
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TIP2-1, At3g16240, MYA6.10 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q41951
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM magnesium/sodium acetate pH 5.0 and 28% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.593
11K, H, -L20.407
ReflectionResolution: 1.18→44.63 Å / Num. obs: 105884 / % possible obs: 99.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0746 / Rsym value: 0.104 / Net I/σ(I): 12.65
Reflection shellResolution: 1.18→1.22 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.63 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation63.13 Å1.64 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALA3.3.20data scaling
MOLREP11.0.02phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GD8

3gd8


Resolution: 1.18→44.63 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.269 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.004 / ESU R Free: 0.004 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.11538 2030 1.9 %RANDOM
Rwork0.10391 ---
obs0.10413 103853 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.595 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20 Å2
2--1.15 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 1.18→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 0 131 1809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191732
X-RAY DIFFRACTIONr_bond_other_d00.021692
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9532370
X-RAY DIFFRACTIONr_angle_other_deg0.7723.0013822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.565241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85522.85749
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13815227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.836152
X-RAY DIFFRACTIONr_chiral_restr0.0980.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212000
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02394
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr10.88433424
X-RAY DIFFRACTIONr_sphericity_free23.015549
X-RAY DIFFRACTIONr_sphericity_bonded8.80453462
LS refinement shellResolution: 1.178→1.209 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 158 -
Rwork0.384 7360 -
obs--96.87 %

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