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Basic information

Entry
Database: PDB / ID: 7w7r
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 / homologyAquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / channel activity / membrane / Aquaporin 1
Function and homology information
Biological speciesAnabas testudineus (climbing perch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 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 Singapore
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

Downloads & links

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Assembly

Deposited unit
A: Aquaporin 1
B: Aquaporin 1
C: Aquaporin 1
D: Aquaporin 1


Theoretical massNumber of molelcules
Total (without water)102,2074
Polymers102,2074
Non-polymers00
Water00
1
A: Aquaporin 1
C: Aquaporin 1

A: Aquaporin 1
C: Aquaporin 1


Theoretical massNumber of molelcules
Total (without water)102,2074
Polymers102,2074
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area12070 Å2
ΔGint-109 kcal/mol
Surface area29940 Å2
MethodPISA
2
B: Aquaporin 1
D: Aquaporin 1

B: Aquaporin 1
D: Aquaporin 1


Theoretical massNumber of molelcules
Total (without water)102,2074
Polymers102,2074
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area11880 Å2
ΔGint-108 kcal/mol
Surface area29740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.670, 178.100, 177.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Aquaporin 1 / Aquaporin 1aa


Mass: 25551.859 Da / Num. of mol.: 4
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

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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: 4.4 Å3/Da / Density % sol: 72.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: reservoir solution: 0.3M Lithium sulfate, 0.1M ADA (pH 6.5), 30% v/v PEG 400. Prior to setting up the crystallization drops, 4 micro liter of the reservoir solution was mixed with 1 micro ...Details: reservoir solution: 0.3M Lithium sulfate, 0.1M ADA (pH 6.5), 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 Dextran sulfate sodium salt Mr 5000. 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: ESRF / Beamline: ID30B / Wavelength: 0.911647 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911647 Å / Relative weight: 1
ReflectionResolution: 3.46→95.818 Å / Num. all: 23598 / Num. obs: 23598 / % possible obs: 98.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 89.09 Å2 / Rpim(I) all: 0.095 / Rrim(I) all: 0.202 / Rsym value: 0.177 / Net I/av σ(I): 0.6 / Net I/σ(I): 4.5 / Num. measured all: 107214
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.46-3.654.30.8320.91447333670.4320.9420.8321.397.9
3.65-3.874.80.6551.11564632530.3260.7340.6551.799.7
3.87-4.144.70.3691.91434230690.1840.4140.3692.799.8
4.14-4.474.40.2512.71222928020.1280.2830.2513.598.5
4.47-4.894.70.1553.81220726210.0770.1740.1554.899.3
4.89-5.474.70.154.21129323900.0730.1680.155.399.1
5.47-6.324.40.1614.1922420790.0810.1820.1615.697.6
6.32-7.744.70.1045.3853618140.0520.1170.1048.399.3
7.74-10.944.30.0518.7591113890.0280.0580.05111.397.7
10.94-95.8184.10.0890.833538140.0680.1140.08912.997.4

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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: 3.46→84.36 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 40.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2991 1060 5.01 %
Rwork0.2707 20104 -
obs0.2721 21164 88.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 269.5 Å2 / Biso mean: 119.4062 Å2 / Biso min: 60.94 Å2
Refinement stepCycle: final / Resolution: 3.46→84.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6438 0 0 0 6438
Num. residues----887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036559
X-RAY DIFFRACTIONf_angle_d0.7048932
X-RAY DIFFRACTIONf_chiral_restr0.0411091
X-RAY DIFFRACTIONf_plane_restr0.0061117
X-RAY DIFFRACTIONf_dihedral_angle_d9.5633824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.46-3.61750.38571020.3666187567
3.6175-3.80820.36491150.3346210376
3.8082-4.04680.36131410.2989242487
4.0468-4.35920.2931210.2703264193
4.3592-4.79790.29941450.2443270195
4.7979-5.4920.26791270.243276497
5.492-6.91890.31151470.286279997
6.9189-84.360.25391620.2454279794
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)
15.5174-1.07480.93765.9964-4.53859.8695-0.0961-0.5792-0.97840.58910.64111.0317-1.5762-1.4909-0.47950.8848-0.0522-0.17440.83650.19921.6112-20.979-10.5-31.623
24.4689-1.9287-1.09671.0588-1.30756.19040.2407-0.4589-0.70990.3713-0.34790.14980.22590.09430.08810.9753-0.0138-0.42270.5852-0.04461.1081-8.972-14.177-29.122
32.52180.1554-1.47961.6847-3.00195.94240.4039-0.5341-1.49531.329-0.62581.67261.7417-0.440.31061.7163-0.1952-0.61460.719-0.11040.9682-16.762-22.973-24.732
47.56672.09480.16798.01270.42824.7143-0.149-0.1571-0.14480.9324-1.10590.25381.01630.48510.3491.18360.0352-0.07091.064-0.14590.5876-6.913-14.852-17.827
57.99481.55221.1931.21882.09995.9129-0.4119-0.2625-0.05251.04840.0976-0.2075-0.07250.66760.37920.74820.1357-0.44940.9282-0.12361.2352-41.231-52.878-34.736
65.2788-3.2388-1.25945.7453.26764.7106-0.232-0.05420.22350.5990.1924-0.1548-0.03410.1642-0.08391.1194-0.0907-0.53080.70960.11041.1214-48.013-52.75-27.145
72.2648-0.95570.29240.39-0.11162.4473-0.452-0.42490.60280.4386-1.16810.0348-1.7321-0.02910.69620.95650.3374-1.4560.70460.34371.6413-47.393-50.131-19.848
81.7035-0.32180.05693.5109-1.92193.41130.67290.38941.00560.0470.64820.3647-1.2817-0.7299-0.22870.99770.2757-1.89210.81110.4633-0.4461-13.21-7.973-66.045
90.5219-1.54941.23544.5345-3.58372.8157-0.6409-0.1009-1.8495-0.4182-0.261-1.90351.94750.76160.8162.6425-0.1917-0.40041.05140.02032.7081-6.236-33.776-54.704
107.2484-0.89341.04881.9295-0.75156.7351-0.64350.38230.73920.0613-0.194-0.0449-0.0266-0.22660.40420.9459-0.026-0.67430.5691-0.00651.2419-14.289-11.86-58.882
119.58542.6377-0.28039.7853-8.93918.68870.32411.838-2.1832-0.7447-1.0999-2.34461.3521.45010.0671.36610.4674-0.94691.102-0.3991.6542-17.293-31.366-56.396
121.9647-0.13260.53840.66740.69671.81720.64010.06470.7006-0.07620.2693-0.5278-0.4615-0.4176-0.03360.1801-0.514-1.62730.3162-0.73932.2779-15.884-12.134-46.544
137.38184.08360.80422.24830.46810.0748-0.38350.5913-1.2185-0.57820.26071.40071.0616-0.61840.07251.2625-0.3365-0.45110.8296-0.49522.672-22.494-24.627-61.865
142.04371.85522.82691.0595-1.20454.8284-0.1547-0.42690.68140.14070.8362-0.1895-0.8706-0.3328-0.12940.2229-0.0707-0.54490.7256-0.19752.1532-25.881-7.779-47.257
156.72321.9331-1.14120.6498-1.16367.7573-0.02550.6990.0683-0.4183-0.25470.1122-0.1759-0.34460.23990.7985-0.0933-0.17510.723-0.08410.4703-44.05-56.892-64.379
165.91242.5744-1.39742.4617-2.80294.054-0.2190.2078-0.75430.3144-0.00270.2326-0.6109-0.3590.1221.23430.0831-0.29580.52180.07751.2965-50.545-48.072-53.136
175.67583.4328-1.27412.1127-0.4284.3158-0.4097-0.3088-1.54710.33860.50480.40590.70670.79050.20811.08670.3114-0.10640.8790.07451.5276-37.88-56.669-61.73
181.55330.2029-0.04450.0204-0.0147-0.0149-0.28561.75131.9236-0.88680.23820.8474-1.0866-0.4109-0.09040.3985-0.87410.08290.7580.18362.9365-45.554-34.193-63.339
197.38722.84324.35441.08811.66552.53170.2810.37630.2212-0.47380.1510.0784-0.21450.9134-0.45231.7714-0.2069-0.29250.6945-0.03730.9796-37.243-37.032-53.361
206.39712.4186-0.99851.38350.1133.2407-0.2761-0.0455-1.3895-0.4394-0.3636-0.38890.1812-0.03150.20040.7235-0.1513-0.31440.6861-0.10361.52-40.823-54.199-46.856
216.31053.7532-3.84482.2308-2.28882.3404-1.03842.18710.9315-1.79291.0858-0.2239-1.12050.0348-0.03411.6458-0.3519-0.760.7989-0.13191.7074-37.499-45.518-61.398
222.17812.0604-1.76737.7927-2.5374.8407-0.1738-0.45250.4502-1.1806-0.0343-0.80220.82330.35360.13721.4857-0.0948-0.53480.6809-0.14522.7528-30.971-52.895-51.124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:34 )A2 - 34
2X-RAY DIFFRACTION2( CHAIN A AND RESID 38:180 )A38 - 180
3X-RAY DIFFRACTION3( CHAIN A AND RESID 181:197 )A181 - 197
4X-RAY DIFFRACTION4( CHAIN A AND RESID 198:221 )A198 - 221
5X-RAY DIFFRACTION5( CHAIN B AND RESID 4:62 )B4 - 62
6X-RAY DIFFRACTION6( CHAIN B AND RESID 63:180 )B63 - 180
7X-RAY DIFFRACTION7( CHAIN B AND RESID 181:221 )B181 - 221
8X-RAY DIFFRACTION8( CHAIN C AND RESID 3:31 )C3 - 31
9X-RAY DIFFRACTION9( CHAIN C AND RESID 32:39 )C32 - 39
10X-RAY DIFFRACTION10( CHAIN C AND RESID 40:109 )C40 - 109
11X-RAY DIFFRACTION11( CHAIN C AND RESID 110:126 )C110 - 126
12X-RAY DIFFRACTION12( CHAIN C AND RESID 127:184 )C127 - 184
13X-RAY DIFFRACTION13( CHAIN C AND RESID 185:202 )C185 - 202
14X-RAY DIFFRACTION14( CHAIN C AND RESID 203:226 )C203 - 226
15X-RAY DIFFRACTION15( CHAIN D AND RESID 0:34 )D0 - 34
16X-RAY DIFFRACTION16( CHAIN D AND RESID 37:63 )D37 - 63
17X-RAY DIFFRACTION17( CHAIN D AND RESID 64:107 )D64 - 107
18X-RAY DIFFRACTION18( CHAIN D AND RESID 108:117 )D108 - 117
19X-RAY DIFFRACTION19( CHAIN D AND RESID 118:124 )D118 - 124
20X-RAY DIFFRACTION20( CHAIN D AND RESID 125:184 )D125 - 184
21X-RAY DIFFRACTION21( CHAIN D AND RESID 185:192 )D185 - 192
22X-RAY DIFFRACTION22( CHAIN D AND RESID 193:224 )D193 - 224

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