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- PDB-3cn6: Crystal structure of the Spinach Aquaporin SoPIP2;1 S274E mutant -

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Basic information

Entry
Database: PDB / ID: 3cn6
TitleCrystal structure of the Spinach Aquaporin SoPIP2;1 S274E mutant
ComponentsAquaporin
KeywordsTRANSPORT PROTEIN / membrane protein / aquaporin / Transmembrane / Transport
Function / homology
Function and homology information


water channel activity / plasmodesma / vacuole / 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: 2.95 Å
AuthorsNyblom, M. / Alfredsson, A. / Hallgren, K. / Hedfalk, K. / Neutze, R. / Tornroth-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 25, 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 / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aquaporin
B: Aquaporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4264
Polymers65,2022
Non-polymers2252
Water81145
1
A: Aquaporin
hetero molecules

A: Aquaporin
hetero molecules

A: Aquaporin
hetero molecules

A: Aquaporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8538
Polymers130,4034
Non-polymers4504
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area12660 Å2
ΔGint-167.1 kcal/mol
Surface area31350 Å2
MethodPISA
2
B: Aquaporin
hetero molecules

B: Aquaporin
hetero molecules

B: Aquaporin
hetero molecules

B: Aquaporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8538
Polymers130,4034
Non-polymers4504
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 area12730 Å2
ΔGint-169.7 kcal/mol
Surface area31220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.558, 89.558, 189.271
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-283-

HOH

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Components

#1: Protein Aquaporin


Mass: 32600.793 Da / Num. of mol.: 2 / Mutation: S274E
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: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Reservoir: 0.1M Tris, 0.2M NaCl, 24% PEG400. Reservoir mixed 1:4 with 0.1M CdCl2, and then mixed 1:1 with protein, centrifuged briefly and supernatant used for crystallization, pH 7, VAPOR ...Details: Reservoir: 0.1M Tris, 0.2M NaCl, 24% PEG400. Reservoir mixed 1:4 with 0.1M CdCl2, and then mixed 1:1 with protein, centrifuged briefly and supernatant used for crystallization, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.95→34.86 Å / Num. all: 15560 / Num. obs: 15560 / % possible obs: 100 % / Redundancy: 4 % / Rsym value: 0.155
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 4.2 % / Num. unique all: 2274 / Rsym value: 0.33

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→34.86 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.984 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22985 772 5 %RANDOM
Rwork0.19567 ---
obs0.19736 14788 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.609 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.95→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 0 2 45 3703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223762
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.9355132
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65922130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.85415538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0481514
X-RAY DIFFRACTIONr_chiral_restr0.1260.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.21923
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.22721
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1720.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.2104
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4070.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2751.52452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79123822
X-RAY DIFFRACTIONr_scbond_it3.35231495
X-RAY DIFFRACTIONr_scangle_it4.0684.51310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 80 -
Rwork0.242 1052 -
obs--100 %

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