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- PDB-4f4l: Open Channel Conformation of a Voltage Gated Sodium Channel -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4f4l
TitleOpen Channel Conformation of a Voltage Gated Sodium Channel
ComponentsIon transport protein
KeywordsMETAL TRANSPORT / alpha helical membrane protein / voltage-gated sodium channel / membrane
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity
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
Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsMcCusker, E.C. / Bagneris, C. / Naylor, C.E. / Cole, A.R. / D'Avanzo, N. / Nichols, C.G. / Wallace, B.A.
CitationJournal: Nat Commun / Year: 2012
Title: Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing.
Authors: McCusker, E.C. / Bagneris, C. / Naylor, C.E. / Cole, A.R. / D'Avanzo, N. / Nichols, C.G. / Wallace, B.A.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Ion transport protein
D: Ion transport protein


Theoretical massNumber of molelcules
Total (without water)49,7584
Polymers49,7584
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-44 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.070, 74.080, 107.930
Angle α, β, γ (deg.)90.00, 118.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ion transport protein


Mass: 12439.515 Da / Num. of mol.: 4 / Fragment: pore region (S5-C-terminal domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus (bacteria) / Strain: MC-1 / Gene: A0L5S6, Mmc1_0798 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0L5S6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.6
Details: 30% PEG 400, 0.09 M tri-sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2011 / Details: Si crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.49→95.1 Å / Num. all: 10528 / Num. obs: 8747 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 92.44 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.05 / Net I/σ(I): 22.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
3.49-3.910.90.7173.2929610.75247.8
3.9-4.511.30.3776.7826090.39592.6
4.5-5.511.30.12217.5622130.12899.4
5.5-7.811.10.05138.1717760.05399.4
7.8-9510.30.02577.759870.02796.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
BUSTER2.10.0refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RVY

3rvy


Resolution: 3.49→43.62 Å / Cor.coef. Fo:Fc: 0.8956 / Cor.coef. Fo:Fc free: 0.8951 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2852 431 4.93 %RANDOM
Rwork0.2707 ---
obs0.2713 8747 83.27 %-
Displacement parametersBiso mean: 137.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.1984 Å20 Å26.0199 Å2
2---10.5239 Å20 Å2
3---10.7224 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.576 Å1.187 Å
Refinement stepCycle: LAST / Resolution: 3.49→43.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 0 42 2759
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d834SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes409HARMONIC5
X-RAY DIFFRACTIONt_it2795HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion397SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3784SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2795HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3842HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion22.36
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)Rfactor allNum. reflection all
3.49-3.90.336750.292134547.8
3.9-4.50.3091290.27230092.6
4.5-5.50.3331080.275210199.4
5.5-7.80.296760.28166399.4
7.8-43.60.212435.280.258134590796.40.29441420

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