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- PDB-3cll: Crystal structure of the Spinach Aquaporin SoPIP2;1 S115E mutant -

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Basic information

Entry
Database: PDB / ID: 3cll
TitleCrystal structure of the Spinach Aquaporin SoPIP2;1 S115E mutant
ComponentsAquaporin
KeywordsTRANSPORT PROTEIN / membrane protein / aquaporin / Transmembrane / Transport
Function / homology
Function and homology information


water channel activity / 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 speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNyblom, M. / Alfredsson, A. / Hallgren, K. / Hedfalk, K. / Neutze, R. / Trnroth-Horsefield, S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and functional analysis of SoPIP2;1 mutants adds insight into plant aquaporin gating.
Authors: Nyblom, M. / Frick, A. / Wang, Y. / Ekvall, M. / Hallgren, K. / Hedfalk, K. / Neutze, R. / Tajkhorshid, E. / Tornroth-Horsefield, S.
History
DepositionMar 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 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


Theoretical massNumber of molelcules
Total (without water)32,1301
Polymers32,1301
Non-polymers00
Water1,31573
1
A: Aquaporin

A: Aquaporin

A: Aquaporin

A: Aquaporin


Theoretical massNumber of molelcules
Total (without water)128,5214
Polymers128,5214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area11650 Å2
ΔGint-135.3 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.855, 86.855, 86.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-282-

HOH

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Components

#1: Protein Aquaporin


Mass: 32130.275 Da / Num. of mol.: 1 / Mutation: S115E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Plasmid: pPICZB / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q41372
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 400, 0.1M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.3→61.43 Å / Num. all: 14333 / Num. obs: 14333 / % possible obs: 100 % / Redundancy: 6.8 % / Rsym value: 0.129
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.9 % / Num. unique all: 2108 / Rsym value: 0.316

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z98

1z98


Resolution: 2.3→35.4 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.08 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19269 718 5 %RANDOM
Rwork0.16469 ---
obs0.16612 13615 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.727 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 0 73 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221864
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9352542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6295240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85622.15465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39615269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.509157
X-RAY DIFFRACTIONr_chiral_restr0.1790.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021395
X-RAY DIFFRACTIONr_nbd_refined0.2280.2954
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21322
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.28
X-RAY DIFFRACTIONr_mcbond_it0.9381.51220
X-RAY DIFFRACTIONr_mcangle_it1.58221892
X-RAY DIFFRACTIONr_scbond_it2.333768
X-RAY DIFFRACTIONr_scangle_it3.124.5650
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 52 -
Rwork0.153 1020 -
obs--100 %

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