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- PDB-2o9g: Crystal Structure of AqpZ mutant L170C complexed with mercury. -

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Basic information

Entry
Database: PDB / ID: 2o9g
TitleCrystal Structure of AqpZ mutant L170C complexed with mercury.
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: 1.9 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: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / 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 1.5Dec 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3597
Polymers23,9721
Non-polymers1,3876
Water2,486138
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)101,43628
Polymers95,8874
Non-polymers5,54824
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 area18770 Å2
ΔGint-592 kcal/mol
Surface area29630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.156, 91.156, 77.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-438-

HOH

21A-442-

HOH

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.: 1 / 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: 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.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.34 Å3/Da / Density % sol: 63.19 %
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, 1mM HgCl2, 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: 1.8→64.457 Å / Num. obs: 24884 / % possible obs: 85.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.91.30.5261.4229017410.52641.1
1.9-2.011.60.3312.3432226870.33167.1
2.01-2.152.10.2283.1693733260.22888.6
2.15-2.3230.1853.81051334710.18598.8
2.32-2.553.60.1265.61182432510.126100
2.55-2.853.70.0917.71076829460.091100
2.85-3.293.70.06610.3952026020.066100
3.29-4.023.60.04414.9806722180.044100
4.02-5.693.60.03616.5614817080.036100
5.69-64.423.40.03714.431609340.03797.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å36.04 Å
Translation2.5 Å36.04 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: 1.9→64.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.441 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1167 5.1 %RANDOM
Rwork0.166 ---
obs0.167 23096 92.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.183 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→64.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 44 138 1869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221781
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9622426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9885234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1312255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96515236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.929155
X-RAY DIFFRACTIONr_chiral_restr0.1460.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021309
X-RAY DIFFRACTIONr_nbd_refined0.2190.2965
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21265
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.289
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.212
X-RAY DIFFRACTIONr_mcbond_it0.771.51173
X-RAY DIFFRACTIONr_mcangle_it1.21421804
X-RAY DIFFRACTIONr_scbond_it2.0673712
X-RAY DIFFRACTIONr_scangle_it2.7774.5621
X-RAY DIFFRACTIONr_sphericity_free14.73834
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 46 -
Rwork0.229 1056 -
obs-1102 60.48 %

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