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- PDB-2w1p: 1.4 Angstrom crystal structure of P.pastoris aquaporin, Aqy1, in ... -

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Basic information

Entry
Database: PDB / ID: 2w1p
Title1.4 Angstrom crystal structure of P.pastoris aquaporin, Aqy1, in a closed conformation at pH 8.0
ComponentsAQUAPORIN PIP2-7 7;
KeywordsMEMBRANE PROTEIN / GATING / YEAST
Function / homology
Function and homology information


water channel activity / endoplasmic reticulum membrane / metal ion 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 speciesKOMAGATAELLA PASTORIS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFischer, G. / Kosinska-Eriksson, U. / Aponte-Santamaria, C. / Palmgren, M. / Geijer, C. / Hedfalk, K. / Hohmann, S. / de Groot, B.L. / Neutze, R. / Lindkvist-Petersson, K.
CitationJournal: Plos Biol. / Year: 2009
Title: Crystal Structure of a Yeast Aquaporin at 1.15 A Reveals a Novel Gating Mechanism
Authors: Fischer, G. / Kosinska-Eriksson, U. / Aponte-Santamaria, C. / Palmgren, M. / Geijer, C. / Hedfalk, K. / Hohmann, S. / De Groot, B.L. / Neutze, R. / Lindkvist-Petersson, K.
History
DepositionOct 20, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AQUAPORIN PIP2-7 7;
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1737
Polymers29,9321
Non-polymers1,2406
Water2,396133
1
A: AQUAPORIN PIP2-7 7;
hetero molecules

A: AQUAPORIN PIP2-7 7;
hetero molecules

A: AQUAPORIN PIP2-7 7;
hetero molecules

A: AQUAPORIN PIP2-7 7;
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,69128
Polymers119,7304
Non-polymers4,96224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
Buried area28210 Å2
ΔGint-162.3 kcal/mol
Surface area33960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.929, 90.929, 80.624
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-1279-

CL

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Components

#1: Protein AQUAPORIN PIP2-7 7; / AQY1 / AQUAPORIN


Mass: 29932.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) KOMAGATAELLA PASTORIS (fungus) / Strain: X33 / References: UniProt: F2QVG4
#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF P. PASTORIS AQUAPORIN, AQY1, WAS KINDLY PROVIDED BY PROF JAMES CREGG AND DR ANTHONY JAY SUNGA.

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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: 2.77 Å3/Da / Density % sol: 55.6 % / Description: NONE
Crystal growpH: 8 / Details: 28% PEG600, 0.05 M HEPES PH 8.0, 1.0 MM ZNSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 8, 2007 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.4→64.5 Å / Num. obs: 65261 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 5.3 % / Biso Wilson estimate: 11.235 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J4N

1j4n


Resolution: 1.4→64.282 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.597 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1785 3261 5.11 %RANDOM
Rwork0.1602 ---
obs0.161 64431 99.978 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.401 Å2
Baniso -1Baniso -2Baniso -3
1--0.149 Å20 Å20 Å2
2---0.149 Å20 Å2
3---0.299 Å2
Refinement stepCycle: LAST / Resolution: 1.4→64.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 82 133 2216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222215
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9633035
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3365284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64321.77279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77215290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.361510
X-RAY DIFFRACTIONr_chiral_restr0.070.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021670
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21066
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21589
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2129
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.2117
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6841.51382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00322160
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.423983
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9674.5869
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 236 -
Rwork0.318 4493 -
obs--100 %

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