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- PDB-7pgg: NaVAb1p detergent (DM) -

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Basic information

Entry
Database: PDB / ID: 7pgg
TitleNaVAb1p detergent (DM)
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / ion channel membrane protein transport protein antibody complex / folding
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / identical protein binding
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-VVA / Ion transport protein
Similarity search - Component
Biological speciesAlcanivorax borkumensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsLolicato, M. / Arrigoni, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Quaternary structure independent folding of voltage-gated ion channel pore domain subunits.
Authors: Arrigoni, C. / Lolicato, M. / Shaya, D. / Rohaim, A. / Findeisen, F. / Fong, L.K. / Colleran, C.M. / Dominik, P. / Kim, S.S. / Schuermann, J.P. / DeGrado, W.F. / Grabe, M. / Kossiakoff, A.A. / Minor Jr., D.L.
History
DepositionAug 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7343
Polymers34,2972
Non-polymers4381
Water00
1
A: Ion transport protein
B: Ion transport protein
hetero molecules

A: Ion transport protein
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4686
Polymers68,5934
Non-polymers8752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14090 Å2
ΔGint-152 kcal/mol
Surface area30090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.471, 157.471, 106.394
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain 'A' and ((resid 132 and (name N or name...
221(chain 'B' and (resid 132 through 135 or resid 137...

NCS oper: (Code: givenMatrix: (0.499178619406, 0.499744636522, 0.707867222151), (0.497959927409, 0.503107491957, -0.706341816851), (-0.709123837297, 0.705080243522, 0.00228770032254)Vector: 0. ...NCS oper: (Code: given
Matrix: (0.499178619406, 0.499744636522, 0.707867222151), (0.497959927409, 0.503107491957, -0.706341816851), (-0.709123837297, 0.705080243522, 0.00228770032254)
Vector: 0.0186513051623, -0.0845827936714, 0.62556915973)

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Components

#1: Protein Ion transport protein


Mass: 17148.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcanivorax borkumensis (bacteria) / Gene: ABO_1668 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VNY2
#2: Chemical ChemComp-VVA / 2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}ethyl heptadecanoate


Mass: 437.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44NO6P
Has ligand of interestN
Has protein modificationY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: SeMet labelled NavAb1 purified in DM was concentrated to 13 mg mL-1 and crystallized in 3% PEG300, 0.75M ammonium sulfate.
Temp details: RT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869, 0.97698, 0.97953, 0.95368
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 19, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1158691
20.976981
30.979531
40.953681
ReflectionResolution: 2.85→50 Å / Num. obs: 31433 / % possible obs: 98.99 % / Redundancy: 16.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.169 / Net I/σ(I): 15.4
Reflection shellResolution: 2.852→2.953 Å / Num. unique obs: 3087 / CC1/2: 0.473

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.17.1_3660refinement
Aimlessdata scaling
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.85→14.96 Å / SU ML: 0.4893 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.3194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2781 1582 5.04 %
Rwork0.2664 29820 -
obs0.2669 31402 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.84 Å2
Refinement stepCycle: LAST / Resolution: 2.85→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 21 0 2353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832460
X-RAY DIFFRACTIONf_angle_d2.09243338
X-RAY DIFFRACTIONf_chiral_restr0.0912370
X-RAY DIFFRACTIONf_plane_restr0.0099415
X-RAY DIFFRACTIONf_dihedral_angle_d10.5843334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.940.41891480.41212663X-RAY DIFFRACTION99.57
2.94-3.050.38521470.38142660X-RAY DIFFRACTION99.89
3.05-3.170.41241340.37272682X-RAY DIFFRACTION100
3.17-3.310.37821450.36732661X-RAY DIFFRACTION99.93
3.31-3.480.40141470.34842692X-RAY DIFFRACTION99.86
3.48-3.70.26051490.29332684X-RAY DIFFRACTION99.86
3.7-3.980.25291430.28572691X-RAY DIFFRACTION99.72
3.98-4.370.29241460.28412709X-RAY DIFFRACTION99.58
4.37-4.980.21551410.23872720X-RAY DIFFRACTION99.37
4.98-6.20.2891340.25282778X-RAY DIFFRACTION99.69
6.2-14.960.23961480.20082880X-RAY DIFFRACTION99.9

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