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- PDB-1rc2: 2.5 Angstrom Resolution X-ray Structure of Aquaporin Z -

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Basic information

Entry
Database: PDB / ID: 1rc2
Title2.5 Angstrom Resolution X-ray Structure of Aquaporin Z
ComponentsAquaporin Z
KeywordsMEMBRANE PROTEIN / aquaporin
Function / homology
Function and homology information


water channel activity / intracellular water homeostasis / water transport / response to osmotic stress / identical protein binding / plasma membrane
Similarity search - Function
Aquaporin Z / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSavage, D.F. / Egea, P.F. / Robles, Y.C. / O'Connell III, J.D. / Stroud, R.M.
CitationJournal: Plos Biol. / Year: 2003
Title: Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z
Authors: Savage, D.F. / Egea, P.F. / Robles-Colmenares, Y. / O'Connell III, J.D. / Stroud, R.M.
History
DepositionNov 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 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
B: Aquaporin Z
A: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6056
Polymers47,4352
Non-polymers1,1694
Water2,342130
1
B: Aquaporin Z
hetero molecules

B: Aquaporin Z
hetero molecules

B: Aquaporin Z
hetero molecules

B: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,54920
Polymers94,8714
Non-polymers4,67816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area15330 Å2
ΔGint-147 kcal/mol
Surface area28800 Å2
MethodPISA, PQS
2
A: Aquaporin Z


Theoretical massNumber of molelcules
Total (without water)23,7181
Polymers23,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Aquaporin Z

A: Aquaporin Z

A: Aquaporin Z

A: Aquaporin Z


Theoretical massNumber of molelcules
Total (without water)94,8714
Polymers94,8714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.550, 93.550, 80.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-1054-

HOH

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Components

#1: Protein Aquaporin Z / Bacterial nodulin-like intrinsic protein


Mass: 23717.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AQPZ, BNIP, B0875, C1009, SF0832, S0873 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P60844
#2: Sugar
ChemComp-BGL / 2-O-octyl-beta-D-glucopyranose / 2-O-octyl-beta-D-glucose / 2-O-octyl-D-glucose / 2-O-octyl-glucose


Type: D-saccharide, beta linking / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.71 Å3/Da / Density % sol: 66.82 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: polyethylene glycol, monomethyl ether 2000, 100mM sodium cacodylate, 200mM MgCl2, 4% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
228 %PEG2000 MME1reservoir
3100 mMsodium cacodylate1reservoirpH6.5
4200 mM1reservoirMgCl2
54 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 9 / Detector: CCD / Date: May 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 27408 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.068 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.38 Å / Num. unique all: 2401 / % possible all: 77.7
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 89.9 % / Num. measured all: 58536 / Rmerge(I) obs: 0.0638
Reflection shell
*PLUS
% possible obs: 90.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J4N

1j4n


Resolution: 2.5→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.268 1504 -
Rwork0.227 --
all-24157 -
obs-21720 89.9 %
Displacement parametersBiso mean: 66.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 80 130 3530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d20
LS refinement shellResolution: 2.5→2.66 Å
RfactorNum. reflection% reflection
Rfree0.38 246 -
Rwork0.313 --
obs-3374 90.7 %
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 6.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20

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