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- PDB-7stc: AQP5 T41H with Ni2+ -

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Basic information

Entry
Database: PDB / ID: 7stc
TitleAQP5 T41H with Ni2+
ComponentsAquaporin-5
KeywordsMEMBRANE PROTEIN / Inhibitor Ni2+
Function / homology
Function and homology information


saliva secretion / Passive transport by Aquaporins / pancreatic juice secretion / water transport / water channel activity / cellular hypotonic response / camera-type eye morphogenesis / odontogenesis / microvillus / basal plasma membrane ...saliva secretion / Passive transport by Aquaporins / pancreatic juice secretion / water transport / water channel activity / cellular hypotonic response / camera-type eye morphogenesis / 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 / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
NICKEL (II) ION / Aquaporin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKowatz, T.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)N000141612535 United States
CitationJournal: To Be Published
Title: AQP5 T41H with Ni2+
Authors: Kowatz, T. / Lodowski, D. / Vahedi-Faridi, A.
History
DepositionNov 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation_author
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)113,8035
Polymers113,7454
Non-polymers591
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-138 kcal/mol
Surface area33210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.681, 90.649, 184.767
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aquaporin-5 / AQP-5


Mass: 28436.188 Da / Num. of mol.: 4 / Mutation: T41H
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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.3 Å3/Da / Density % sol: 62.74 % / Description: needle
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M Tris-HCl, pH 7.6, 0.1 M NaCl, 18% PEG400. 6% 1,6 hexanediol (v/v), 3% 1,3 propanediol (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→34.22 Å / Num. obs: 71938 / % possible obs: 99 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rpim(I) all: 0.166 / Net I/σ(I): 3.6
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 6.6 % / Num. unique obs: 4395 / CC1/2: 0.088 / Rpim(I) all: 2.793 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D9S

3d9s


Resolution: 2.25→34.22 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.862 / SU R Cruickshank DPI: 0.271 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.264 / SU Rfree Blow DPI: 0.22 / SU Rfree Cruickshank DPI: 0.225
RfactorNum. reflection% reflectionSelection details
Rfree0.3105 3029 -RANDOM
Rwork0.2864 ---
obs0.2874 71704 99.3 %-
Displacement parametersBiso mean: 57.92 Å2
Baniso -1Baniso -2Baniso -3
1--17.4761 Å20 Å20 Å2
2--5.5389 Å20 Å2
3---11.9372 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.25→34.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7240 0 1 171 7412
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087416HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8810128HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2340SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1216HARMONIC5
X-RAY DIFFRACTIONt_it7416HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion996SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6444SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion17.61
LS refinement shellResolution: 2.25→2.27 Å
RfactorNum. reflection% reflection
Rfree0.5311 62 -
Rwork0.52 --
obs0.5205 1435 99.72 %

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