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- PDB-3ne2: Archaeoglobus fulgidus aquaporin -

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Basic information

Entry
Database: PDB / ID: 3ne2
TitleArchaeoglobus fulgidus aquaporin
ComponentsProbable aquaporin AqpM
KeywordsTRANSPORT PROTEIN / transmembrane helices / water channel / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP
Function / homology
Function and homology information


water channel activity / 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
Probable aquaporin AqpM
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsLee, J.K. / Finer-Moore, J.S. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: To be Published
Title: Archaeoglobus fulgidus aquaporin
Authors: Lee, J.K. / Finer-Moore, J.S. / Stroud, R.M.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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 / 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 1.4Sep 6, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable aquaporin AqpM
B: Probable aquaporin AqpM
C: Probable aquaporin AqpM
D: Probable aquaporin AqpM
E: Probable aquaporin AqpM
F: Probable aquaporin AqpM
G: Probable aquaporin AqpM
H: Probable aquaporin AqpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,40417
Polymers201,7738
Non-polymers2,6319
Water52229
1
A: Probable aquaporin AqpM
B: Probable aquaporin AqpM
C: Probable aquaporin AqpM
D: Probable aquaporin AqpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3489
Polymers100,8864
Non-polymers1,4625
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17430 Å2
ΔGint-144 kcal/mol
Surface area29150 Å2
MethodPISA
2
E: Probable aquaporin AqpM
F: Probable aquaporin AqpM
G: Probable aquaporin AqpM
H: Probable aquaporin AqpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0568
Polymers100,8864
Non-polymers1,1694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15760 Å2
ΔGint-159 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.899, 199.861, 90.567
Angle α, β, γ (deg.)90.000, 117.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 3 - 245 / Label seq-ID: 3 - 245

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
DetailsThe biological unit is a tetramer. There are two tetramers in the asymmetric unit. Chains A,B,C, and D comprise one tetramer and chains E,F,G, and H comprise the second.

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Components

#1: Protein
Probable aquaporin AqpM


Mass: 25221.607 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: aqpM, AF_1426 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: O28846
#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.: 9
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 63.58 %

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 4, 2007 / Details: monochrometer
RadiationMonochromator: Khozu double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 35301 / Num. obs: 35301 / % possible obs: 54.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.6
Reflection shellResolution: 2.8→2.8 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.4 / Num. unique all: 820 / % possible all: 12.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ELVESrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Accession code 2F2B

2f2b


Resolution: 3→39.07 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.841 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.25 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.71 / SU B: 55.475 / SU ML: 0.453 / SU R Cruickshank DPI: 0.577 / SU Rfree: 0.659 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.659 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY TLS refinement - each chain a separate group, strict NCS restraints for all chains
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1693 5.1 %RANDOM
Rwork0.245 ---
all0.246 33177 --
obs0.246 33177 61.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 191.47 Å2 / Biso mean: 141.86 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å20.64 Å2
2--0.36 Å2-0 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 3→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14029 0 180 29 14238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02214569
X-RAY DIFFRACTIONr_bond_other_d0.0020.029291
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.97719928
X-RAY DIFFRACTIONr_angle_other_deg0.953322794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0351947
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86422.762420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.354151934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.911540
X-RAY DIFFRACTIONr_chiral_restr0.0580.22392
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116285
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023027
X-RAY DIFFRACTIONr_mcbond_it0.241.59583
X-RAY DIFFRACTIONr_mcbond_other0.081.54086
X-RAY DIFFRACTIONr_mcangle_it0.392215241
X-RAY DIFFRACTIONr_scbond_it0.55334986
X-RAY DIFFRACTIONr_scangle_it0.9194.54687
Refine LS restraints NCS

Ens-ID: 1 / Number: 2831 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.040.05
2BTIGHT POSITIONAL0.030.05
3CTIGHT POSITIONAL0.040.05
4DTIGHT POSITIONAL0.030.05
5ETIGHT POSITIONAL0.030.05
6FTIGHT POSITIONAL0.040.05
7GTIGHT POSITIONAL0.030.05
8HTIGHT POSITIONAL0.030.05
1ATIGHT THERMAL0.070.5
2BTIGHT THERMAL0.050.5
3CTIGHT THERMAL0.060.5
4DTIGHT THERMAL0.050.5
5ETIGHT THERMAL0.040.5
6FTIGHT THERMAL0.070.5
7GTIGHT THERMAL0.040.5
8HTIGHT THERMAL0.050.5
LS refinement shellResolution: 2.996→3.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.491 48 -
Rwork0.367 923 -
all-971 -
obs--24.65 %
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)
11.7737-0.24570.535810.2455-1.35732.31610.15750.1538-0.0022-1.2827-0.01530.3543-0.3559-0.0301-0.14220.448-0.0339-0.0560.25910.01140.0311-1.30833.713-2.515
22.41440.39970.05858.6351-0.65673.63750.0345-0.18390.34872.57110.25491.9123-0.9776-0.5051-0.28941.47630.14920.48160.33330.03170.4858-11.95540.15821.978
30.441-0.9217-0.548110.4593-1.61484.6190.05410.08290.08780.4925-0.4207-3.0232-0.3520.55690.36660.105-0.1104-0.22820.39640.10181.07521.20724.1319.65
42.0739-0.77520.66568.1923-0.96852.4683-0.1126-0.41070.18693.36980.0847-2.0413-0.9848-0.11990.02793.0298-0.1092-0.79330.2558-0.04530.532810.98930.94734.203
52.5801-1.41170.5228.65990.02754.0553-0.2446-0.2432-0.04451.94080.27013.44970.1003-0.5992-0.02550.5527-0.04780.67440.59460.11.6161-21.048-11.29524.024
61.7415-1.0109-0.332210.0849-0.61892.7120.22030.0210.0241-1.1308-0.04850.34970.3996-0.0737-0.17180.3396-0.0788-0.13270.2448-0.02190.07970.333-19.5069.024
73.16880.2905-0.3077.63120.24632.3485-0.0936-0.6312-0.31464.46350.23381.147-0.0137-0.3041-0.14013.4852-0.03170.56830.63060.14020.2654-7.078-16.99747.066
82.5371-0.210.57799.93-0.60942.68290.0731-0.3318-0.02432.2618-0.0643-1.79210.55350.2914-0.00881.4078-0.0178-0.67240.4410.01180.407214.46-24.96531.858
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999

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