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- PDB-7nl4: OsNIP2;1 silicon transporter from rice -

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Basic information

Entry
Database: PDB / ID: 7nl4
TitleOsNIP2;1 silicon transporter from rice
ComponentsAquaporin NIP2-1
KeywordsMEMBRANE PROTEIN / Aquaporin Membrane transporter Metalloids OsNIP2 / 1
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
Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
: / Aquaporin NIP2-1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
Authorsvan den Berg, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural Basis for Silicic Acid Uptake by Higher Plants.
Authors: van den Berg, B. / Pedebos, C. / Bolla, J.R. / Robinson, C.V. / Basle, A. / Khalid, S.
History
DepositionFeb 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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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)192,86017
Polymers191,8488
Non-polymers1,0129
Water00
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)96,59810
Polymers95,9244
Non-polymers6746
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-153 kcal/mol
Surface area25600 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)96,2617
Polymers95,9244
Non-polymers3373
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13340 Å2
ΔGint-149 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.888, 96.692, 99.787
Angle α, β, γ (deg.)63.91, 71.16, 65.07
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 23981.000 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: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q6Z2T3
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
Has ligand of interestN

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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: 3.7 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28-32% PEG400 1 mM CdCl2 30 mM MgCl2.6H2O 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.107 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.107 Å / Relative weight: 1
ReflectionResolution: 2.616→82.01 Å / Num. obs: 48853 / % possible obs: 91.8 % / Redundancy: 3.4 % / CC1/2: 0.98 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 6.2
Reflection shellResolution: 2.616→2.91 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4644 / CC1/2: 0.9 / Rsym value: 0.619 / % possible all: 79.6

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EVU

2evu


Resolution: 3→48.78 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 2157 4.79 %
Rwork0.2378 --
obs0.24 44991 78.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12820 0 9 0 12829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01313179
X-RAY DIFFRACTIONf_angle_d2.01918020
X-RAY DIFFRACTIONf_dihedral_angle_d18.0231790
X-RAY DIFFRACTIONf_chiral_restr0.092166
X-RAY DIFFRACTIONf_plane_restr0.0132204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.3447710.31721191X-RAY DIFFRACTION33
3.07-3.150.3694640.2871500X-RAY DIFFRACTION41
3.15-3.230.3502860.29661716X-RAY DIFFRACTION47
3.23-3.330.3565930.28242061X-RAY DIFFRACTION57
3.33-3.430.34021090.29922344X-RAY DIFFRACTION65
3.43-3.560.34271370.3052676X-RAY DIFFRACTION74
3.56-3.70.30121650.27333083X-RAY DIFFRACTION86
3.7-3.870.311570.25393543X-RAY DIFFRACTION97
3.87-4.070.28512000.2263536X-RAY DIFFRACTION99
4.07-4.330.26431840.21483555X-RAY DIFFRACTION98
4.33-4.660.27381600.21393554X-RAY DIFFRACTION98
4.66-5.130.24831890.19873545X-RAY DIFFRACTION98
5.13-5.870.2982010.23223531X-RAY DIFFRACTION98
5.87-7.390.28921530.24983559X-RAY DIFFRACTION98
7.39-48.780.23661880.22153440X-RAY DIFFRACTION96
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)
11.77740.093-0.19092.3287-0.86151.7077-0.18890.19050.1555-0.2412-0.0988-0.5474-0.63460.85040.10140.4057-0.26960.03430.52320.09580.3472-25.399-18.221-33.848
21.21580.72770.33171.16910.12740.92330.04730.1009-0.0673-0.2940.17520.42720.5972-0.70910.19410.8455-0.6484-0.19931.02380.08360.4678-56.065-42.888-29.26
31.5695-0.2374-0.36231.0465-0.00580.8083-0.00660.15510.4030.04650.23410.5524-0.6675-0.9558-0.08130.620.46620.05050.86250.22430.6957-52.659-15.159-28.278
41.6764-0.31080.21371.9060.45830.1595-0.00650.495-0.4293-0.41090.0946-0.42760.80490.5944-0.30581.14850.29220.1750.5776-0.19040.579-28.894-46.147-34.97
52.0016-0.1839-0.21412.1702-0.12150.61860.1254-0.0075-0.44420.0719-0.2454-0.63140.9820.8947-0.04960.66520.3804-0.11780.59910.09090.6064-22.035-50.611.266
60.9666-0.1179-0.06831.59270.60991.40010.0381-0.29880.48110.5615-0.05440.2338-0.7456-0.29440.04821.17520.20160.08420.3307-0.15380.5441-41.319-16.27617.029
71.65950.43090.10992.1783-0.84392.26660.077-0.0994-0.18260.26330.22310.49150.3392-1.2738-0.30060.4138-0.2280.00390.5930.07320.3203-48.437-43.617.091
81.72530.71420.37791.2050.48050.851-0.08910.0050.1020.1728-0.1257-0.4027-0.6070.9685-0.08730.6622-0.5203-0.25840.95480.13430.6118-14.786-23.28311.498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 45:260 )E45 - 260
2X-RAY DIFFRACTION2( CHAIN F AND RESID 45:260 )F45 - 260
3X-RAY DIFFRACTION3( CHAIN G AND RESID 45:260 )G45 - 260
4X-RAY DIFFRACTION4( CHAIN H AND RESID 45:260 )H45 - 260
5X-RAY DIFFRACTION5( CHAIN A AND RESID 45:260 )A45 - 260
6X-RAY DIFFRACTION6( CHAIN B AND RESID 45:260 )B45 - 260
7X-RAY DIFFRACTION7( CHAIN C AND RESID 45:258 )C45 - 258
8X-RAY DIFFRACTION8( CHAIN D AND RESID 45:260 )D45 - 260

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