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- PDB-3zoj: High-resolution structure of Pichia Pastoris aquaporin Aqy1 at 0.88 A -

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Basic information

Entry
Database: PDB / ID: 3zoj
TitleHigh-resolution structure of Pichia Pastoris aquaporin Aqy1 at 0.88 A
ComponentsAQUAPORIN
KeywordsMEMBRANE PROTEIN / CHANNEL
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: 0.88 Å
AuthorsKosinska-Eriksson, U. / Fischer, G. / Friemann, R. / Enkavi, G. / Tajkhorshid, E. / Neutze, R.
Citation
Journal: Science / Year: 2013
Title: Subangstrom Resolution X-Ray Structure Details Aquaporin-Water Interactions
Authors: Kosinska-Eriksson, U. / Fischer, G. / Friemann, R. / Enkavi, G. / Tajkhorshid, E. / Neutze, R.
#1: Journal: Plos Biol. / Year: 2009
Title: Crystal Structure of a Yeast Aquaporin at 1.15 Angstrom 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
DepositionFeb 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _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 2.1Dec 20, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AQUAPORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9167
Polymers29,9321
Non-polymers9836
Water3,819212
1
A: AQUAPORIN
hetero molecules

A: AQUAPORIN
hetero molecules

A: AQUAPORIN
hetero molecules

A: AQUAPORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,66428
Polymers119,7304
Non-polymers3,93424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area26590 Å2
ΔGint-205.6 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.763, 90.763, 80.311
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-1277-

CL

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Components

#1: Protein AQUAPORIN / AQUAPORIN PIP2-7 7


Mass: 29932.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KOMAGATAELLA PASTORIS (fungus) / Strain: X33 / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): 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.: 3
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.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCHLORIDE ION (CL): ASSIGNED BASED ON DIFFERENCE DENSITY AND CHEMICAL SANITY B-OCTYLGLUCOSIDE (BOG): ...CHLORIDE ION (CL): ASSIGNED BASED ON DIFFERENCE DENSITY AND CHEMICAL SANITY B-OCTYLGLUCOSIDE (BOG): ONLY ASSIGNED WHEN HEADGROUP WAS UNAMBIGUOUSLY VISIBLE IN THE DENSITY.

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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: 2 LOW-, 2 MEDIUM- AND 3 HIGH-RESOLUTION DATASETS WERE COLLECTED FROM A SINGLE CRYSTAL.
Crystal growpH: 8 / Details: 26% PEG600, 100 MM TRIS (PH=8.0), 200 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.65
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 0.88→64 Å / Num. obs: 252057 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.2
Reflection shellResolution: 0.88→0.93 Å / Redundancy: 11 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W2E

2w2e


Resolution: 0.88→60.15 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.206 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.009 / ESU R Free: 0.009 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. POLAR HYDROGENS WERE SET TO OCCUPANCY 0 UNLESS THEY WERE OBSERVED IN THE DIFFERENCE DENSITY. HYDROGEN ATOMS FOR WATERS IN THE CHANNEL CAN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. POLAR HYDROGENS WERE SET TO OCCUPANCY 0 UNLESS THEY WERE OBSERVED IN THE DIFFERENCE DENSITY. HYDROGEN ATOMS FOR WATERS IN THE CHANNEL CAN BE OBSERVED THROUGH THE DIFFERENCE DENSITY BUT HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.10739 2381 0.9 %RANDOM
Rwork0.10325 ---
obs0.10329 249442 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.806 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 0.88→60.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 63 212 2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192243
X-RAY DIFFRACTIONr_bond_other_d0.0010.022150
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9533073
X-RAY DIFFRACTIONr_angle_other_deg0.8723.0014902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9215286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0821.88285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48515305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0841512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02568
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9010.8661105
X-RAY DIFFRACTIONr_mcbond_other0.8730.8641104
X-RAY DIFFRACTIONr_mcangle_it1.0551.3031398
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6921.1211138
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.42334393
X-RAY DIFFRACTIONr_sphericity_free16.2650.552
X-RAY DIFFRACTIONr_sphericity_bonded8.0060.54475
LS refinement shellResolution: 0.8846→0.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 53 -
Rwork0.248 18437 -
obs--99.44 %

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