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- PDB-3c02: X-ray structure of the aquaglyceroporin from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 3c02
TitleX-ray structure of the aquaglyceroporin from Plasmodium falciparum
ComponentsAquaglyceroporin
KeywordsMEMBRANE PROTEIN / glycerol / water / transport / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Porin / Transmembrane
Function / homology
Function and homology information


glucosylglycerol transmembrane transport / Transport of glycerol from adipocytes to the liver by Aquaporins / Vasopressin regulates renal water homeostasis via Aquaporins / Passive transport by Aquaporins / polyol transmembrane transporter activity / polyol transmembrane transport / glycerol transmembrane transporter activity / glycerol channel activity / glycolipid biosynthetic process / urea transmembrane transporter activity ...glucosylglycerol transmembrane transport / Transport of glycerol from adipocytes to the liver by Aquaporins / Vasopressin regulates renal water homeostasis via Aquaporins / Passive transport by Aquaporins / polyol transmembrane transporter activity / polyol transmembrane transport / glycerol transmembrane transporter activity / glycerol channel activity / glycolipid biosynthetic process / urea transmembrane transporter activity / urea transmembrane transport / glycerol transmembrane transport / water transport / water channel activity / ammonium channel activity / identical protein binding / plasma membrane
Similarity search - Function
: / Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNewby, Z.E. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum.
Authors: Newby, Z.E. / O'Connell, J. / Robles-Colmenares, Y. / Khademi, S. / Miercke, L.J. / Stroud, R.M.
History
DepositionJan 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 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

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Assembly

Deposited unit
A: Aquaglyceroporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0727
Polymers28,3191
Non-polymers7536
Water1,00956
1
A: Aquaglyceroporin
hetero molecules

A: Aquaglyceroporin
hetero molecules

A: Aquaglyceroporin
hetero molecules

A: Aquaglyceroporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,28828
Polymers113,2764
Non-polymers3,01124
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 area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.430, 92.430, 193.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Aquaglyceroporin


Mass: 28319.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: AQP / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8WPZ6
#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.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 17% PEG MME 2000, 0.1M Sodium citrate, 15% Glycerol, 0.04M n-octyl-B-D-glucopyranoside, 0.01 Nickel sulfate, 0.01M DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2007
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.05→46.2 Å / Num. all: 25478 / Num. obs: 24719 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15 % / Biso Wilson estimate: 47.9 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.06 / Net I/σ(I): 28.8
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.25 / Num. unique all: 1819 / Rsym value: 0.435 / % possible all: 69.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FX8

1fx8


Resolution: 2.05→46.2 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.214 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.134 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19824 1299 5.1 %RANDOM
Rwork0.18088 ---
all0.184 24719 --
obs0.18175 24179 95.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.452 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20 Å2
2--1.51 Å20 Å2
3----3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 50 56 1959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221981
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9752696
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3745253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08323.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64615301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.794154
X-RAY DIFFRACTIONr_chiral_restr0.1260.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021436
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21089
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21457
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8541.51249
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32921958
X-RAY DIFFRACTIONr_scbond_it2.3953846
X-RAY DIFFRACTIONr_scangle_it3.3464.5731
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 67 -
Rwork0.232 1231 -
obs--67.18 %
Refinement TLS params.Method: refined / Origin x: 8.552 Å / Origin y: 19.124 Å / Origin z: 22.738 Å
111213212223313233
T0.2831 Å2-0.0816 Å2-0.0288 Å2-0.1454 Å2-0.1112 Å2--0.0286 Å2
L1.2542 °2-0.1237 °2-0.0528 °2-1.079 °20.0185 °2--1.9651 °2
S-0.0163 Å °-0.3277 Å °0.2916 Å °0.2784 Å °0.0253 Å °-0.1287 Å °-0.519 Å °0.237 Å °-0.0089 Å °

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