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- PDB-7cjs: structure of aquaporin -

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Basic information

Entry
Database: PDB / ID: 7cjs
Titlestructure of aquaporin
ComponentsAquaporin NIP2-1
KeywordsTRANSPORT PROTEIN / aquaporn
Function / homology
Function and homology information


silicate transmembrane transporter activity / silicic acid import across plasma membrane / Casparian strip / channel activity / membrane / 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
CHOLESTEROL HEMISUCCINATE / Aquaporin NIP2-1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSaitoh, Y. / Ma, J.F. / Suga, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for high selectivity of a rice silicon channel Lsi1.
Authors: Saitoh, Y. / Mitani-Ueno, N. / Saito, K. / Matsuki, K. / Huang, S. / Yang, L. / Yamaji, N. / Ishikita, H. / Shen, J.R. / Ma, J.F. / Suga, M.
History
DepositionJul 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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 NIP2-1
B: Aquaporin NIP2-1
C: Aquaporin NIP2-1
D: Aquaporin NIP2-1
E: Aquaporin NIP2-1
F: Aquaporin NIP2-1
G: Aquaporin NIP2-1
H: Aquaporin NIP2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,90633
Polymers216,4438
Non-polymers4,46325
Water17,727984
1
A: Aquaporin NIP2-1
B: Aquaporin NIP2-1
C: Aquaporin NIP2-1
D: Aquaporin NIP2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,84318
Polymers108,2224
Non-polymers2,62114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16640 Å2
ΔGint-147 kcal/mol
Surface area27640 Å2
MethodPISA
2
E: Aquaporin NIP2-1
F: Aquaporin NIP2-1
G: Aquaporin NIP2-1
H: Aquaporin NIP2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,06415
Polymers108,2224
Non-polymers1,84211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15930 Å2
ΔGint-149 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.568, 92.453, 166.126
Angle α, β, γ (deg.)90.000, 102.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEFGH

#1: Protein
Aquaporin NIP2-1 / Low silicon protein 1 / NOD26-like intrinsic protein 2-1 / OsNIP2 / 1 / Silicon influx transporter LSI1


Mass: 27055.389 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: NIP2-1, LSI1, SIIT1, Os02g0745100, LOC_Os02g51110, OJ1118_G04.16, OJ1734_E02.43, OsJ_008085
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6Z2T3
#3: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 1005 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 984 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Nonpolymer detailsPG4 was modeled as PEG400.

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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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: PEG 400, Gly-NaOH, octyl-glucoside, and cholesteryl hemisuccinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.11218 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11218 Å / Relative weight: 1
ReflectionResolution: 1.8→19.838 Å / Num. obs: 237514 / % possible obs: 96.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 23.63 Å2 / CC1/2: 0.996 / Net I/σ(I): 5.73
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 37334 / CC1/2: 0.784

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ne2

3ne2


Resolution: 1.8→19.838 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2732 11430 4.89 %
Rwork0.2447 222235 -
obs0.2461 233665 95.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.31 Å2 / Biso mean: 30.9367 Å2 / Biso min: 16.6 Å2
Refinement stepCycle: final / Resolution: 1.8→19.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12845 0 568 984 14397
Biso mean--67.53 39.8 -
Num. residues----1731
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82040.39883730.4083690190
1.8204-1.84180.42643540.4017710592
1.8418-1.86430.40853690.3934725093
1.8643-1.88790.43193730.3726725594
1.8879-1.91270.36083860.3478726795
1.9127-1.93890.35343730.3381739795
1.9389-1.96650.35133820.3332731895
1.9665-1.99590.34974120.3162738396
1.9959-2.0270.33093650.3101742496
2.027-2.06020.3193760.3009738796
2.0602-2.09570.32693570.2927740695
2.0957-2.13380.32133750.2853744396
2.1338-2.17480.31733960.2824738896
2.1748-2.21910.31743780.2799743896
2.2191-2.26730.2934050.276738496
2.2673-2.320.32153880.2642742096
2.32-2.37790.27443720.2538746496
2.3779-2.44210.29443590.2513745996
2.4421-2.51380.25974040.2363745996
2.5138-2.59480.26493910.2279743996
2.5948-2.68730.27433720.2352751897
2.6873-2.79460.2494170.2222747996
2.7946-2.92140.24773840.2216751197
2.9214-3.07490.23153830.2197742496
3.0749-3.26680.23123730.2142747896
3.2668-3.51770.27624010.2211747596
3.5177-3.86930.22743870.198755597
3.8693-4.42380.21883620.1954758497
4.4238-5.55320.2433710.2147761297
5.5532-19.8380.2463920.2298761296
Refinement TLS params.Method: refined / Origin x: -9.5384 Å / Origin y: 44.777 Å / Origin z: 33.43 Å
111213212223313233
T0.2146 Å2-0.0048 Å20.1282 Å2-0.1906 Å20.0216 Å2--0.2073 Å2
L0.0982 °20.0383 °20.0793 °2-0.1201 °20.0988 °2--0.2152 °2
S-0.0082 Å °0.0258 Å °0.0203 Å °-0.0579 Å °0.0003 Å °-0.0266 Å °0.001 Å °-0.0036 Å °0.0045 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA46 - 258
2X-RAY DIFFRACTION1allA301 - 401
3X-RAY DIFFRACTION1allB46 - 264
4X-RAY DIFFRACTION1allB301 - 401
5X-RAY DIFFRACTION1allC46 - 259
6X-RAY DIFFRACTION1allC301 - 401
7X-RAY DIFFRACTION1allD46 - 264
8X-RAY DIFFRACTION1allD301 - 401
9X-RAY DIFFRACTION1allE46 - 259
10X-RAY DIFFRACTION1allE301 - 401
11X-RAY DIFFRACTION1allF46 - 264
12X-RAY DIFFRACTION1allF301 - 401
13X-RAY DIFFRACTION1allG46 - 259
14X-RAY DIFFRACTION1allG301 - 401
15X-RAY DIFFRACTION1allH46 - 264
16X-RAY DIFFRACTION1allH301 - 401
17X-RAY DIFFRACTION1allS1 - 1045

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