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- PDB-7w7s: High resolution structure of a fish aquaporin reveals a novel ext... -

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Basic information

Entry
Database: PDB / ID: 7w7s
TitleHigh resolution structure of a fish aquaporin reveals a novel extracellular fold.
ComponentsAquaporin 1
KeywordsMEMBRANE PROTEIN / Aquaporin / fish / Anabas testudineus / Pichia pastoris / transport protein
Function / homology
Function and homology information


renal water transport / carbon dioxide transmembrane transporter activity / glycerol transmembrane transporter activity / water channel activity / ammonium channel activity / hyperosmotic response / 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 speciesAnabas testudineus (climbing perch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZeng, J. / Schmitz, F. / Isaksson, S. / Glas, J. / Arbab, O. / Andersson, M. / Sundell, K. / Eriksson, L. / Swaminathan, K. / Tornroth-Horsefield, S. / Hedfalk, K.
Funding support Sweden, Singapore, 6items
OrganizationGrant numberCountry
Swedish Research CouncilK2013-66X-20431-07-05 Sweden
Swedish Research Council2009-00360 Sweden
Swedish Research Council2013-05945 Sweden
Ministry of Education (MoE, Singapore)R154-000-632-112 Singapore
National Research Foundation (NRF, Singapore)R706-000-041-279 Sweden
Swedish Research Council FORMAS2012-771 Sweden
CitationJournal: Life Sci Alliance / Year: 2022
Title: High-resolution structure of a fish aquaporin reveals a novel extracellular fold.
Authors: Zeng, J. / Schmitz, F. / Isaksson, S. / Glas, J. / Arbab, O. / Andersson, M. / Sundell, K. / Eriksson, L.A. / Swaminathan, K. / Tornroth-Horsefield, S. / Hedfalk, K.
History
DepositionDec 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aquaporin 1


Theoretical massNumber of molelcules
Total (without water)25,5521
Polymers25,5521
Non-polymers00
Water2,234124
1
A: Aquaporin 1

A: Aquaporin 1

A: Aquaporin 1

A: Aquaporin 1


Theoretical massNumber of molelcules
Total (without water)102,2074
Polymers102,2074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
Buried area10780 Å2
ΔGint-100 kcal/mol
Surface area29310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.060, 80.060, 95.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-386-

HOH

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Components

#1: Protein Aquaporin 1 / Aquaporin 1aa


Mass: 25551.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabas testudineus (climbing perch) / Gene: aqp1aa, aqp1 / Production host: Komagataella pastoris (fungus) / References: UniProt: M1K561
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: reservoir solution: 0.1M Tris-HCl (pH 7.8). 5% w/v gamma-PGA (Na+ form, LM), 30% v/v PEG 400. Prior to setting up the crystallization drops, 4 micro liter of the reservoir solution was mixed ...Details: reservoir solution: 0.1M Tris-HCl (pH 7.8). 5% w/v gamma-PGA (Na+ form, LM), 30% v/v PEG 400. Prior to setting up the crystallization drops, 4 micro liter of the reservoir solution was mixed with 1 micro liter 30% w/v D-Sorbitol. Crystallization drops were set up by mixing the reservoir/additive mixture with protein at 1:1 or 2:1 ratio and the drops were left to equilibrate against 0.5 milliliter reservoir at room temperature and crystal grew in cold room (4 degree)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.9→95.28 Å / Num. all: 25108 / Num. obs: 25108 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 25.19 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.114 / Rsym value: 0.108 / Net I/av σ(I): 1.3 / Net I/σ(I): 15.1 / Num. measured all: 305910
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs
1.9-212.10.6571.24358735880.1950.6860.6574
2-2.1212.90.5351.54351533770.1550.5570.5355.1
2.12-2.2712.30.39523970832330.1170.4130.3956.6
2.27-2.4511.70.25633509729950.0780.2680.2569.4
2.45-2.6912.80.1754.33537527610.0510.1820.17513.4
2.69-312.10.1275.93062725360.0380.1330.12717.4
3-3.4712.30.07992743022370.0230.0820.07925
3.47-4.2512.20.05312.12359119270.0160.0550.05335.3
4.25-6.0111.40.04712.41747915300.0150.050.04737.8
6.01-95.2810.30.0661.295019240.0330.0760.06637.5

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J4N

1j4n


Resolution: 1.9→61.294 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 1305 5.2 %
Rwork0.1779 23773 -
obs0.1792 25078 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.35 Å2 / Biso mean: 36.3923 Å2 / Biso min: 14.03 Å2
Refinement stepCycle: final / Resolution: 1.9→61.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 0 124 1718
Biso mean---47.51 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141623
X-RAY DIFFRACTIONf_angle_d1.1712207
X-RAY DIFFRACTIONf_chiral_restr0.086269
X-RAY DIFFRACTIONf_plane_restr0.01275
X-RAY DIFFRACTIONf_dihedral_angle_d10.228948
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9-1.97610.27631330.27992594
1.9761-2.0660.29261310.23522591
2.066-2.1750.21171540.19672593
2.175-2.31120.1981470.16462591
2.3112-2.48970.17431590.13862607
2.4897-2.74020.16711360.13722629
2.7402-3.13670.18381460.14892633
3.1367-3.95190.20011400.16052692
3.9519-61.2940.20081590.19822843
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.79380.206-5.25163.314-0.30448.12920.3004-0.53540.34280.33-0.08880.616-0.4429-0.1876-0.28710.19020.00640.02160.2395-0.05730.42615.18885.89225.69
24.9271.1803-2.78630.4668-1.16952.945-1.01861.3622-0.1363-1.46560.6461.32130.0607-0.52950.37221.1032-0.2451-0.6360.85920.03032.324430.09281.3020.624
31.99690.3020.0071.72340.58682.3838-0.0139-0.19140.04830.0163-0.09220.3312-0.0849-0.32090.0730.1301-0.00040.01740.1836-0.01380.319518.99879.87122.782
45.445-5.7959-4.87686.82184.93934.4670.09840.40310.9677-1.4301-0.20210.2435-1.0284-0.3743-0.01090.45550.0276-0.17980.2586-0.01470.502219.63274.112.946
52.66260.17151.79171.06790.25972.79390.0585-0.2275-0.09990.055-0.02260.14960.1985-0.3126-0.0650.1352-0.02360.01940.15030.00880.265422.37269.9719.746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:33 )A2 - 33
2X-RAY DIFFRACTION2( CHAIN A AND RESID 34:43 )A34 - 43
3X-RAY DIFFRACTION3( CHAIN A AND RESID 44:108 )A44 - 108
4X-RAY DIFFRACTION4( CHAIN A AND RESID 114:127 )A114 - 127
5X-RAY DIFFRACTION5( CHAIN A AND RESID 128:226 )A128 - 226

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