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- PDB-2o9d: Crystal Structure of AqpZ mutant T183C. -

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Basic information

Entry
Database: PDB / ID: 2o9d
TitleCrystal Structure of AqpZ mutant T183C.
ComponentsAquaporin Z
KeywordsMEMBRANE PROTEIN / aquaporin / integral membrane protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP
Function / homology
Function and homology information


intracellular water homeostasis / water transport / water channel activity / 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
octyl alpha-L-altropyranoside / Aquaporin Z
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSavage, D.F. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural basis of aquaporin inhibition by mercury.
Authors: Savage, D.F. / Stroud, R.M.
History
DepositionDec 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / pdbx_validate_chiral / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_validate_chiral.auth_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Dec 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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)48,8455
Polymers47,9682
Non-polymers8773
Water1,72996
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)99,44416
Polymers95,9364
Non-polymers3,50812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area13790 Å2
ΔGint-161 kcal/mol
Surface area28370 Å2
MethodPISA, PQS
2
B: Aquaporin Z


Theoretical massNumber of molelcules
Total (without water)23,9841
Polymers23,9841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Aquaporin Z

B: Aquaporin Z

B: Aquaporin Z

B: Aquaporin Z


Theoretical massNumber of molelcules
Total (without water)95,9364
Polymers95,9364
Non-polymers00
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
MethodPQS
Unit cell
Length a, b, c (Å)92.428, 92.428, 78.235
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-285-

HOH

21B-273-

HOH

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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 4

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ARGARGBB-1 - 2302 - 233
2LYSLYSAA-1 - 2292 - 232

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Components

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


Mass: 23983.875 Da / Num. of mol.: 2 / Mutation: C9S,C20S,T183C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aqpZ, bniP / Production host: Escherichia coli (E. coli) / References: UniProt: P60844
#2: Sugar ChemComp-HSG / octyl alpha-L-altropyranoside / octyl alpha-L-altroside / octyl L-altroside / octyl altroside


Type: L-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6
#3: Sugar ChemComp-HSH / octyl beta-D-galactopyranoside / octyl beta-D-galactoside / octyl D-galactoside / octyl galactoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.48 Å3/Da / Density % sol: 64.68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: hanging drop with 1:1 addition of protien and mothor liquor, 25% polyethylene glycol monomethyl ether 2000, 100 mM sodium cacodylate, 100 mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.3→92.45 Å / Num. obs: 28901 / % possible obs: 98.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.422.80.5951.21135540040.59593.8
2.42-2.572.90.37121119739050.37196.6
2.57-2.752.90.33611082637210.33698.7
2.75-2.973.20.1973.51139935460.19799.9
2.97-3.253.50.1295.41153432650.129100
3.25-3.643.70.0946.11102429700.094100
3.64-4.23.80.0627.5982926060.062100
4.2-5.143.90.04713.6866422240.047100
5.14-7.273.90.03717.7664217240.037100
7.27-92.453.60.03316.533399360.03396.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å92.43 Å
Translation2.5 Å92.43 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→92.45 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 16.283 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1472 5.1 %RANDOM
Rwork0.197 ---
obs0.199 28884 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.666 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2---1.04 Å20 Å2
3---2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→92.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 60 96 3512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223510
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9574781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1365462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.322.037108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.89615463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.108159
X-RAY DIFFRACTIONr_chiral_restr0.1180.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022593
X-RAY DIFFRACTIONr_nbd_refined0.2080.21795
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.2144
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3660.210
X-RAY DIFFRACTIONr_mcbond_it1.21622320
X-RAY DIFFRACTIONr_mcangle_it1.84333576
X-RAY DIFFRACTIONr_scbond_it1.17521385
X-RAY DIFFRACTIONr_scangle_it1.56231205
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 1649 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.290.5
MEDIUM THERMAL0.822
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 97 -
Rwork0.298 1887 -
obs-1984 92.32 %
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)
11.8684-0.0118-0.31962.0070.32361.2737-0.06370.26540.3599-0.2776-0.12010.3487-0.3126-0.32350.18390.0490.114-0.11750.02790.01390.15933.0202-31.8196-9.7309
21.60350.0444-0.38351.80270.39474.2940.1195-0.4558-0.46250.53730.2384-0.27671.22030.6085-0.35780.31640.1946-0.24270.04710.02090.18728.7562-17.445928.414
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-1 - 2292 - 232
22BB-1 - 2312 - 234

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