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- PDB-2o9e: Crystal Structure of AqpZ mutant T183C complexed with mercury -

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Basic information

Entry
Database: PDB / ID: 2o9e
TitleCrystal Structure of AqpZ mutant T183C 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


water channel activity / intracellular water homeostasis / 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 / Resolution: 2.2 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 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aquaporin Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5194
Polymers23,9171
Non-polymers6023
Water1,11762
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)98,07416
Polymers95,6674
Non-polymers2,40712
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 area16040 Å2
ΔGint-455 kcal/mol
Surface area26830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.103, 91.103, 77.944
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-253-

HOH

21A-254-

HOH

31A-258-

HOH

41A-275-

HOH

51A-276-

HOH

61A-277-

HOH

71A-278-

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: 23916.807 Da / Num. of mol.: 1 / 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: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.39 Å3/Da / Density % sol: 63.72 %
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, 1 mM 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: 2.2→64.42 Å / Num. obs: 16199 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.323.50.5940.8827423500.594100
2.32-2.463.50.3931.8788222300.393100
2.46-2.633.50.2562.6739521030.256100
2.63-2.843.50.1932.3685819560.193100
2.84-3.113.50.1315.2640718090.131100
3.11-3.483.50.0867.7568716380.086100
3.48-4.023.40.0599.9495414460.059100
4.02-4.923.40.04912.7414712220.04999.9
4.92-6.963.30.04114.431399430.04199.6
6.96-64.423.10.03714.215535020.03793.7

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å64.42 Å
Translation2.5 Å64.42 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: 2.2→64.42 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.55 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 815 5 %RANDOM
Rwork0.193 ---
obs0.196 16195 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→64.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 3 62 1735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221717
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.9442343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1715231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86121.73152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87215229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.729155
X-RAY DIFFRACTIONr_chiral_restr0.1220.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021291
X-RAY DIFFRACTIONr_nbd_refined0.2180.2874
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21231
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.25
X-RAY DIFFRACTIONr_mcbond_it0.8731.51160
X-RAY DIFFRACTIONr_mcangle_it1.45521788
X-RAY DIFFRACTIONr_scbond_it1.983654
X-RAY DIFFRACTIONr_scangle_it2.6424.5555
X-RAY DIFFRACTIONr_sphericity_free16.9932
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 66 -
Rwork0.265 1122 -
obs-1188 99.83 %

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