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- PDB-2o9f: Crystal Structure of AqpZ mutant L170C -

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Basic information

Entry
Database: PDB / ID: 2o9f
TitleCrystal Structure of AqpZ mutant L170C
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aquaporin Z
B: Aquaporin Z


Theoretical massNumber of molelcules
Total (without water)47,9442
Polymers47,9442
Non-polymers00
Water77543
1
A: Aquaporin Z

A: Aquaporin Z

A: Aquaporin Z

A: Aquaporin Z


Theoretical massNumber of molelcules
Total (without water)95,8874
Polymers95,8874
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
Buried area14490 Å2
ΔGint-155 kcal/mol
Surface area28060 Å2
MethodPISA, PQS
2
B: Aquaporin Z


Theoretical massNumber of molelcules
Total (without water)23,9721
Polymers23,9721
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)95,8874
Polymers95,8874
Non-polymers00
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
MethodPQS
Unit cell
Length a, b, c (Å)91.333, 91.333, 77.504
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
DetailsThe biological assembly is a tetramer generated from the monomer by the operations X,Y,Z ; -X,-Y,Z ; -Y,X,Z ; and Y,-X,Z

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Components

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


Mass: 23971.820 Da / Num. of mol.: 2 / Mutation: C9S,C20S,L170C
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.38 Å3/Da / Density % sol: 63.61 %
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
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONALS 8.3.11
2
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.55→91.29 Å / Num. obs: 15207 / % possible obs: 74.1 % / Rsym value: 0.075

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å77.5 Å
Translation2.5 Å77.5 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: 2.55→91.29 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.884 / SU B: 20.915 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.432 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 790 5.2 %RANDOM
Rwork0.236 ---
obs0.238 15207 72.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.913 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2--1.21 Å20 Å2
3----2.41 Å2
Refinement stepCycle: LAST / Resolution: 2.55→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 0 43 3407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223462
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9394719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75721.927109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.53415472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1741510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022598
X-RAY DIFFRACTIONr_nbd_refined0.2320.21844
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22424
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.2136
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.50.26
X-RAY DIFFRACTIONr_mcbond_it0.4351.52315
X-RAY DIFFRACTIONr_mcangle_it0.73723581
X-RAY DIFFRACTIONr_scbond_it1.07631339
X-RAY DIFFRACTIONr_scangle_it1.6314.51138
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 62 -
Rwork0.317 934 -
obs-996 64.51 %
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)
11.54140.1411-0.27550.82660.10370.411-0.0042-0.02640.16850.0274-0.02230.1942-0.0897-0.11950.02640.13520.0348-0.00680.148-0.01920.2231-15.821211.426510.3392
21.13960.0961-0.08261.154-0.03180.3595-0.00990.0068-0.19270.0293-0.0104-0.26560.04830.1510.02030.120.0367-0.00730.16390.01250.2387-29.529134.5409-28.2357
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: -1 - 230 / Label seq-ID: 2 - 233

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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