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- PDB-4jc6: Mercury activation of the plant aquaporin SoPIP2;1 - structural a... -

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Basic information

Entry
Database: PDB / ID: 4jc6
TitleMercury activation of the plant aquaporin SoPIP2;1 - structural and functional characterization
ComponentsAquaporin
KeywordsTRANSPORT PROTEIN / Membrane protein / aquaporin / mercury / cadmium
Function / homology
Function and homology information


water channel activity / plasmodesma / vacuole / identical protein binding / plasma membrane
Similarity search - Function
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 speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.152 Å
AuthorsFrick, A. / Jarva, M. / Nyblom, M. / Ekvall, M. / Uzdavinys, P. / Tornroth-Horsefield, S.
CitationJournal: Biochem.J. / Year: 2013
Title: Mercury increases water permeability of a plant aquaporin through a non-cysteine-related mechanism.
Authors: Frick, A. / Jarva, M. / Ekvall, M. / Uzdavinys, P. / Nyblom, M. / Tornroth-Horsefield, S.
History
DepositionFeb 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: 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 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aquaporin
B: Aquaporin
C: Aquaporin
D: Aquaporin
H: Aquaporin
J: Aquaporin
L: Aquaporin
N: Aquaporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,56970
Polymers239,4398
Non-polymers12,13162
Water11,097616
1
A: Aquaporin
B: Aquaporin
C: Aquaporin
D: Aquaporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,69535
Polymers119,7194
Non-polymers5,97531
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19560 Å2
ΔGint-606 kcal/mol
Surface area31880 Å2
MethodPISA
2
H: Aquaporin
J: Aquaporin
L: Aquaporin
N: Aquaporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,87535
Polymers119,7194
Non-polymers6,15531
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20600 Å2
ΔGint-597 kcal/mol
Surface area32220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.546, 141.818, 186.515
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51H
61J
71L
81N

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Components

#1: Protein
Aquaporin


Mass: 29929.814 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Production host: Pichia pastoris (fungus) / References: UniProt: Q41372
#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.: 13
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cd
#4: Chemical...
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Hg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The protein was incubated with 5mM HgCl2, and excess HgCl2 was washed away. Crystallisation condition was 26% PEG400, 25mM Tris pH 7.0, 100mM NaCl. The precipitant solution was mixed with ...Details: The protein was incubated with 5mM HgCl2, and excess HgCl2 was washed away. Crystallisation condition was 26% PEG400, 25mM Tris pH 7.0, 100mM NaCl. The precipitant solution was mixed with 1/5 0.1M CdCl2. Protein and precipitant solution was mixed in 1:1 ratio , VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 176544 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.15-2.235.60.639198.9
2.23-2.325.90.463199.6
2.32-2.426.10.3751100
2.42-2.556.10.3011100
2.55-2.716.10.2371100
2.71-2.926.10.1911100
2.92-3.216.10.1411100
3.21-3.675.90.111199.6
3.67-4.635.90.0861100
4.63-305.90.069199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å29.89 Å
Translation4 Å29.89 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z98

1z98


Resolution: 2.152→29.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.12 / SU B: 3.751 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1685 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22704 8822 5 %RANDOM
Rwork0.19693 ---
obs0.19843 167468 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.716 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å2-0 Å2
2--2.15 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.152→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15026 0 309 616 15951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915742
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.95321445
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64252005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12522520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.345152221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1681556
X-RAY DIFFRACTIONr_chiral_restr0.0880.22500
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111556
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7742.9648035
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.634.4310035
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6033.3177707
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A961MEDIUM POSITIONAL0.10.5
2B961MEDIUM POSITIONAL0.080.5
3C961MEDIUM POSITIONAL0.080.5
4D961MEDIUM POSITIONAL0.080.5
5H961MEDIUM POSITIONAL0.080.5
6J961MEDIUM POSITIONAL0.080.5
7L961MEDIUM POSITIONAL0.080.5
8N961MEDIUM POSITIONAL0.080.5
1A841LOOSE POSITIONAL0.355
2B841LOOSE POSITIONAL0.285
3C841LOOSE POSITIONAL0.295
4D841LOOSE POSITIONAL0.245
5H841LOOSE POSITIONAL0.265
6J841LOOSE POSITIONAL0.325
7L841LOOSE POSITIONAL0.235
8N841LOOSE POSITIONAL0.285
1A961MEDIUM THERMAL2.232
2B961MEDIUM THERMAL3.612
3C961MEDIUM THERMAL1.822
4D961MEDIUM THERMAL2.232
5H961MEDIUM THERMAL3.762
6J961MEDIUM THERMAL2.522
7L961MEDIUM THERMAL2.172
8N961MEDIUM THERMAL1.772
1A841LOOSE THERMAL2.9610
2B841LOOSE THERMAL4.4310
3C841LOOSE THERMAL2.6710
4D841LOOSE THERMAL2.8810
5H841LOOSE THERMAL4.3510
6J841LOOSE THERMAL3.0310
7L841LOOSE THERMAL2.8510
8N841LOOSE THERMAL2.6710
LS refinement shellResolution: 2.152→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 673 -
Rwork0.249 11817 -
obs--96.08 %

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