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- PDB-3nk5: Crystal structure of AqpZ mutant F43W -

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Basic information

Entry
Database: PDB / ID: 3nk5
TitleCrystal structure of AqpZ mutant F43W
ComponentsAquaporin Z
KeywordsTRANSPORT PROTEIN / aquaporin / integral membrane protein / selectivity filter
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: 2.4 Å
AuthorsSavage, D.F. / O'Connell, J.D. / Stroud, R.M. / Finer-Moore, J.S.
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 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software
Item: _audit_author.name / _software.classification / _software.name
Revision 1.3Jul 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 1.4Feb 21, 2024Group: 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 / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)49,1596
Polymers47,9902
Non-polymers1,1694
Water2,450136
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)99,48816
Polymers95,9804
Non-polymers3,50812
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 area14220 Å2
ΔGint-161 kcal/mol
Surface area28430 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)97,1498
Polymers95,9804
Non-polymers1,1694
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 area18480 Å2
ΔGint-129 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.424, 92.424, 78.819
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-286-

HOH

21B-256-

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
DetailsThe biological assembly is a tetramer and can be generated from either chain in the structure by the 4-fold crystallographic symmetry axis: (X,Y,Z), (-X,-Y,Z), (-Y,X,Z), (Y,-X,Z)

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Components

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


Mass: 23994.967 Da / Num. of mol.: 2 / Fragment: Chains A and B / Mutation: F43W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aqpZ, b0875, bniP, JW0859 / Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25-30% PEG2000,100mM sodium cacodylate, 50-100mM 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: 2.4→92.45 Å / Num. all: 24848 / Num. obs: 24848 / % possible obs: 95.4 % / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.532.90.6991.1958932810.69986.6
2.53-2.682.90.4731.6942432520.47391.7
2.68-2.8730.3072.4946631870.30794.7
2.87-3.13.10.1983.7947730500.19896.8
3.1-3.393.30.1215.9918328230.12197.8
3.39-3.793.40.0828.6880626220.08299.7
3.79-4.383.50.05711.7819623220.057100
4.38-5.373.50.04614.3679319490.04699.9
5.37-7.593.60.03717.4565615520.037100
7.59-19.9923.80.02520.231048100.02594.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.99 Å
Translation2.5 Å19.99 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.21data scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ELVESrefinement
ELVESdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 209F

209f


Resolution: 2.4→19.99 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2052 / WRfactor Rwork: 0.1741 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8868 / SU B: 14.28 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2787 / SU Rfree: 0.2128 / Isotropic thermal model: individual restrained / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1264 5.1 %RANDOM
Rwork0.1812 ---
obs0.1831 24847 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.39 Å2 / Biso mean: 49.589 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 80 136 3572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223532
X-RAY DIFFRACTIONr_bond_other_d0.0020.022283
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.964812
X-RAY DIFFRACTIONr_angle_other_deg1.16135575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05422.037108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73915465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.568159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213917
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02772
X-RAY DIFFRACTIONr_mcbond_it0.6461.52256
X-RAY DIFFRACTIONr_mcbond_other0.1921.5974
X-RAY DIFFRACTIONr_mcangle_it1.13523564
X-RAY DIFFRACTIONr_scbond_it1.98531276
X-RAY DIFFRACTIONr_scangle_it2.914.51248
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2730 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.050.05
TIGHT THERMAL0.170.5
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 81 -
Rwork0.305 1556 -
all-1637 -
obs--84.64 %
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)
11.5948-0.0522-0.34641.8035-0.04291.358-0.04530.27520.2961-0.2614-0.06420.2502-0.2478-0.3070.10950.10640.0631-0.09610.10960.00230.1594-13.406314.2462-9.9462
21.502-0.0998-0.07021.92360.23223.52370.1849-0.3164-0.37760.32540.2562-0.25841.06810.5188-0.44110.39060.1446-0.2290.1608-0.01850.2321-37.584228.786827.7814
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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