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- PDB-2w2e: 1.15 Angstrom crystal structure of P.pastoris aquaporin, Aqy1, in... -

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Basic information

Entry
Database: PDB / ID: 2w2e
Title1.15 Angstrom crystal structure of P.pastoris aquaporin, Aqy1, in a closed conformation at pH 3.5
ComponentsAQUAPORIN PIP2-7 7
KeywordsMEMBRANE PROTEIN / YEAST / GATING
Function / homology
Function and homology information


channel activity / endoplasmic reticulum membrane / metal ion binding
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: 1.15 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.1.15 A
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 29, 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 / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / 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 1.4Dec 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)31,79310
Polymers29,9321
Non-polymers1,8619
Water2,576143
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)127,17240
Polymers119,7304
Non-polymers7,44236
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area28610 Å2
ΔGint-173.1 kcal/mol
Surface area37450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.447, 91.447, 80.819
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-1281-

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 / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 6
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 / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.43 Å3/Da / Density % sol: 49.4 % / Description: NONE
Crystal growpH: 3.5
Details: 28% PEG400, 100 MM SODIUM CITRATE PH=3.5, 200 MM LITHIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 8, 2007 / Details: MIRRORS
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.15→20 Å / Num. obs: 111455 / % possible obs: 94.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.31
Reflection shellResolution: 1.15→1.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.16 / % possible all: 99.1

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J4N

1j4n


Resolution: 1.15→20 Å / Num. parameters: 20766 / Num. restraintsaints: 27331 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: H-ATOMS ADDED TO ALL RESIDUES AS A RIDING MODEL, EXCEPT TO THE ONES SURROUNDING THE WATER CHANNEL TO BE ABLE TO OBSERVE DIFFERENCE IN DENSITY. SIDECHAINS OF RESIDUES GLN12, GLU14 AND ARG236 ...Details: H-ATOMS ADDED TO ALL RESIDUES AS A RIDING MODEL, EXCEPT TO THE ONES SURROUNDING THE WATER CHANNEL TO BE ABLE TO OBSERVE DIFFERENCE IN DENSITY. SIDECHAINS OF RESIDUES GLN12, GLU14 AND ARG236 COULD NOT BE OBSERVED WITH SUFFICIENT OCCUPANCY - OCCUPANCY FOR THE NON-OBSERVED ATOMS WAS SET TO 0. SIDE-CHAINS OF RESIDUES ASP77 AND ARG123 COULD ONLY BE OBSERVED WITH PARTIAL OCCUPANCY AND THUS SET TO AN OCCUPANCY OF 0.5. 10 N-TERMINAL AND 6 C-TERMINAL RESIDUES COULD NOT BE OBSERVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.165 5573 5 %RANDOM
obs0.14 -90 %-
all-105882 --
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 1936.39 / Occupancy sum non hydrogen: 2192.03
Refinement stepCycle: LAST / Resolution: 1.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 123 143 2267
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.023
X-RAY DIFFRACTIONs_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.01
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.034
X-RAY DIFFRACTIONs_approx_iso_adps0.125

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