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- PDB-3d9s: Human Aquaporin 5 (AQP5) - High Resolution X-ray Structure -

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Basic information

Entry
Database: PDB / ID: 3d9s
TitleHuman Aquaporin 5 (AQP5) - High Resolution X-ray Structure
ComponentsAquaporin-5
KeywordsMEMBRANE PROTEIN / Aquaporin / AQP / Aquaglyceroporin / water transport / lipid / Phosphatidylserine / PSF / NPA / ar/R / Water channel / Glycoprotein / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


Passive transport by Aquaporins / saliva secretion / pancreatic juice secretion / water transport / water channel activity / camera-type eye morphogenesis / cellular hypotonic response / odontogenesis / microvillus / basal plasma membrane ...Passive transport by Aquaporins / saliva secretion / pancreatic juice secretion / water transport / water channel activity / camera-type eye morphogenesis / cellular hypotonic response / odontogenesis / microvillus / basal plasma membrane / cytoplasmic vesicle membrane / carbon dioxide transport / protein homotetramerization / apical plasma membrane / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Aquaporin 5 / 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
Chem-PS6 / Aquaporin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 2 Å
AuthorsHorsefield, R. / Norden, K. / Fellert, M. / Backmark, A. / Tornroth-Horsefield, S. / Terwisscha Van Scheltinga, A.C. / Kvassman, J. / Kjellbom, P. / Johanson, U. / Neutze, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: High-resolution x-ray structure of human aquaporin 5
Authors: Horsefield, R. / Norden, K. / Fellert, M. / Backmark, A. / Tornroth-Horsefield, S. / Terwisscha van Scheltinga, A.C. / Kvassman, J. / Kjellbom, P. / Johanson, U. / Neutze, R.
History
DepositionMay 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aquaporin-5
B: Aquaporin-5
C: Aquaporin-5
D: Aquaporin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1645
Polymers113,5974
Non-polymers5681
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13190 Å2
ΔGint-132 kcal/mol
Surface area32430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.477, 90.644, 184.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aquaporin-5 / AQP-5


Mass: 28399.145 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: EasySelect Pichia Expression Kit (Invitrogen) / Gene: AQP5 / Plasmid: pPICZB / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P55064
#2: Chemical ChemComp-PS6 / O-[(S)-{[(2S)-2-(hexanoyloxy)-3-(tetradecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-D-serine


Mass: 567.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H50NO10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPS6 IS A MODIFIED FORM OF PHOSPHATIDYLSERINE (PSF).

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 19% polyethylene glycol 400, 0.1M Tris HCl pH 7.6, 0.1M NaCl, 6% v/v 1,6-hexanediol, 3% v/v 1,4-butanediol or 3% v/v 1,3-propanediol, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→52.56 Å / Num. all: 84751 / Num. obs: 84751 / % possible obs: 82.9 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 26.15 Å2 / Rsym value: 0.061 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 12232 / Rsym value: 0.494 / % possible all: 82.6

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 1J4N

1j4n


Resolution: 2→10 Å / Num. parameters: 29577 / Num. restraintsaints: 30558 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: Engh & Huber
Details: Firstly, a homology model for AQP5 was generated using the SWISS-MODEL web server with the bovine AQP1 structure (PDB 1J4N) as a template. The homology model was then used as search model in ...Details: Firstly, a homology model for AQP5 was generated using the SWISS-MODEL web server with the bovine AQP1 structure (PDB 1J4N) as a template. The homology model was then used as search model in molecular replacement calculations. See primary citation for additional details.; This data is merohedrally twinned; THE TWINNING OPERATOR IS (H,K,L) -> (k, h, -l) AND THE TWINNING FRACTION IS 0.463. Diffraction data was from a crystal with near-perfect pseudo-merohedral twinning with the twin operator(010 100 00-1)swapping the a and b axes. Therefore, conventional programs/maps are not recommended when analysing this PDB and structure factors. ShelX (with BASF and TWIN values set) is useful for map calculation but the twinning compatible scripts are best for reliable omit maps (see Supporting Information of primary citation).
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4174 -THIN RESOLUTION SHELLS (RANDOMLY) TO ACCOUNT FOR TWINNING; TWIN RELATED REFLECTIONS ALWAYS IN THE SAME SET (WORK OR TEST SET) NOT DIVIDED BETWEEN THEM.
Rwork0.162 ---
all-84751 --
obs-79673 78 %-
Displacement parametersBiso mean: 37.2 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7386.58
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7241 0 38 111 7390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0241
X-RAY DIFFRACTIONs_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.103
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 2→2.11 Å / Rfactor Rfree: 0.193 / Rfactor Rwork: 0.162

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