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- PDB-5c5x: CRYSTAL STRUCTURE OF THE S156E MUTANT OF HUMAN AQUAPORIN 5 -

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Basic information

Entry
Database: PDB / ID: 5c5x
TitleCRYSTAL STRUCTURE OF THE S156E MUTANT OF HUMAN AQUAPORIN 5
ComponentsAquaporin-5
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


saliva secretion / Passive transport by Aquaporins / pancreatic juice secretion / water transport / cellular hypotonic response / camera-type eye morphogenesis / water channel activity / odontogenesis / microvillus / basal plasma membrane ...saliva secretion / Passive transport by Aquaporins / pancreatic juice secretion / water transport / cellular hypotonic response / camera-type eye morphogenesis / water channel activity / odontogenesis / microvillus / basal plasma membrane / carbon dioxide transport / cytoplasmic vesicle membrane / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKitchen, P. / Oeberg, F. / Sjoehamn, J. / Hedfalk, K. / Bill, R.M. / Conner, A.C. / Conner, M.T. / Toernroth-Horsefield, S.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council0114 225 3004 Sweden
Swedish Research Council2010-5208 Sweden
CitationJournal: Plos One / Year: 2015
Title: Plasma Membrane Abundance of Human Aquaporin 5 Is Dynamically Regulated by Multiple Pathways.
Authors: Kitchen, P. / Oberg, F. / Sjohamn, J. / Hedfalk, K. / Bill, R.M. / Conner, A.C. / Conner, M.T. / Tornroth-Horsefield, S.
History
DepositionJun 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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-5
B: Aquaporin-5
C: Aquaporin-5
D: Aquaporin-5
E: Aquaporin-5
F: Aquaporin-5
G: Aquaporin-5
H: Aquaporin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,19410
Polymers206,0588
Non-polymers1,1352
Water14,340796
1
A: Aquaporin-5
B: Aquaporin-5
C: Aquaporin-5
D: Aquaporin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5975
Polymers103,0294
Non-polymers5681
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13190 Å2
ΔGint-131 kcal/mol
Surface area34550 Å2
MethodPISA
2
E: Aquaporin-5
F: Aquaporin-5
G: Aquaporin-5
H: Aquaporin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5975
Polymers103,0294
Non-polymers5681
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13060 Å2
ΔGint-134 kcal/mol
Surface area34770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.750, 170.750, 189.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Aquaporin-5 / AQP-5


Mass: 25757.299 Da / Num. of mol.: 8 / Mutation: S156E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP5 / Production host: Komagataella pastoris (fungus) / 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.: 2 / Source method: obtained synthetically / Formula: C26H50NO10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: RESERVOIR SOLUTION (100MM TRIS-HCL PH7.9, 100MM NACL, 21% PEG400) MIXED WITH EACH OF 1,6-HEXANEDIOL (30%, V/V) AND 1,3-PROPANEDIOL (40%, V/V) AND MIXED WITH THE TEMPERATURE 281K
PH range: 7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 8, 2010
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.6→50.81 Å / Num. obs: 94885 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.18 / Rsym value: 0.156 / Net I/σ(I): 7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.671 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D9S

3d9s


Resolution: 2.6→50.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.868 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4754 5 %RANDOM
Rwork0.193 ---
obs0.195 94885 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.53 Å20 Å2
2--1.07 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14447 0 56 796 15299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02214850
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.951.97120291
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.30751944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.3122.86479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.972152174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2341556
X-RAY DIFFRACTIONr_chiral_restr0.0630.22460
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210966
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.27786
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.210824
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2752
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3131.59970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.564215486
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.60335618
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0184.54805
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: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 359 -
Rwork0.248 6711 -
obs--99.42 %

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