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- PDB-3nka: Crystal structure of AqpZ H174G,T183F -

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Basic information

Entry
Database: PDB / ID: 3nka
TitleCrystal structure of AqpZ H174G,T183F
ComponentsAquaporin Z
KeywordsTRANSPORT PROTEIN / aquaporin / integral membrane protein / selectivity filter mutants
Function / homology
Function and homology information


intracellular water homeostasis / water channel activity / 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 / molecular replacement / Resolution: 2.5 Å
AuthorsSavage, D.F. / O'Connell III, J.D. / Finer-Moore, J. / Stroud, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural context shapes the aquaporin selectivity filter.
Authors: Savage, D.F. / O'Connell, J.D. / Miercke, L.J. / Finer-Moore, J. / Stroud, R.M.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 6, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aquaporin Z
B: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4049
Polymers47,9582
Non-polymers1,4467
Water1,35175
1
A: Aquaporin Z
hetero molecules

A: Aquaporin Z
hetero molecules

A: Aquaporin Z
hetero molecules

A: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,16124
Polymers95,9164
Non-polymers4,24520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area16030 Å2
ΔGint-168 kcal/mol
Surface area29020 Å2
MethodPISA
2
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)97,45412
Polymers95,9164
Non-polymers1,5388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area19430 Å2
ΔGint-139 kcal/mol
Surface area30530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.784, 92.784, 78.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-260-

HOH

21A-267-

HOH

31A-268-

HOH

41A-282-

HOH

51A-283-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 1 - 228 / Label seq-ID: 4 - 231

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 23978.941 Da / Num. of mol.: 2 / Fragment: chains A and B / Mutation: H174G, T183F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aqpZ, b0875, bniP, JW0859 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P60844
#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.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.54 Å3/Da / Density % sol: 65.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25-30% PEG 2000 100 mM sodium cacodylate 50-100 mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2006 / Details: monochrometer
RadiationMonochromator: Khozu double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→92.848 Å / Num. all: 21743 / Num. obs: 21743 / % possible obs: 93.8 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 17.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.643.50.6451.2959127430.64582.4
2.64-2.83.30.4221.7903327060.42285.8
2.8-2.993.20.2872.7889827620.28792.7
2.99-3.233.20.1714.4871327140.17197.4
3.23-3.543.30.1086.7854125590.10898.7
3.54-3.953.40.0678.7803723370.06799.9
3.95-4.563.50.03917724420710.039100
4.56-5.593.40.03419.5589817480.03499.7
5.59-7.913.60.02821.9491813790.028100
7.91-20.0643.70.0223.726587240.0293.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å20 Å
Translation2.5 Å20 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.21data scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ELVESrefinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O9F

2o9f


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2091 / WRfactor Rwork: 0.1746 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8818 / SU B: 16.579 / SU ML: 0.168 / SU R Cruickshank DPI: 0.3571 / SU Rfree: 0.2375
Isotropic thermal model: restrained atomic B-factors with TLS
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 1120 5.2 %RANDOM
Rwork0.1862 ---
obs0.188 21742 93.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 102.81 Å2 / Biso mean: 55.675 Å2 / Biso min: 2.14 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 98 75 3530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223546
X-RAY DIFFRACTIONr_bond_other_d0.0050.022315
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9684819
X-RAY DIFFRACTIONr_angle_other_deg1.4235648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2595461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02122.11109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17315467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.803159
X-RAY DIFFRACTIONr_chiral_restr0.0950.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213924
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02779
X-RAY DIFFRACTIONr_mcbond_it0.6171.52259
X-RAY DIFFRACTIONr_mcbond_other0.1661.5978
X-RAY DIFFRACTIONr_mcangle_it1.12123565
X-RAY DIFFRACTIONr_scbond_it1.92331287
X-RAY DIFFRACTIONr_scangle_it2.8584.51254
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2735 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.080.05
TIGHT THERMAL0.150.5
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 77 -
Rwork0.343 1268 -
all-1345 -
obs--80.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9290.1554-0.23792.1503-0.12530.8748-0.02-0.38030.37990.3426-0.0457-0.3923-0.27040.27730.06570.1755-0.0764-0.11320.1641-0.04430.172613.520514.195510.4824
21.92380.0689-0.32232.4178-0.0753.02730.18840.4444-0.5355-0.4180.30080.35181.0119-0.5348-0.48920.4522-0.1644-0.31520.20710.00640.314837.579929.0449-27.4178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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