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- PDB-6p6y: Crystal structure of voltage-gated sodium channel NavAb V100C/Q15... -

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Basic information

Entry
Database: PDB / ID: 6p6y
TitleCrystal structure of voltage-gated sodium channel NavAb V100C/Q150C disulfide crosslinked mutant in the activated state
ComponentsIon transport proteinIon transporter
Keywordsmembrane protein / metal transport / Ion channel / ion transport protein
Function / homologyIon transport domain / Voltage-dependent channel domain superfamily / Ion transport protein / ion channel activity / integral component of membrane / identical protein binding / Ion transport protein
Function and homology information
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsWisedchaisri, G. / Tonggu, L. / McCord, E. / Gamal El-din, T.M. / Wang, L. / Zheng, N. / Catterall, W.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and StrokeR01 NS015751 United States
National Institutes of Health/National Heart, Lung, and Blood InstituteR01 HL112808 United States
National Institutes of Health/National Institute of General Medical SciencesT32 GM007750 United States
Howard Hughes Medical Institute United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3938
Polymers29,7681
Non-polymers4,6247
Water0
1
A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,57132
Polymers119,0734
Non-polymers18,49828
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area42270 Å2
ΔGint-243 kcal/mol
Surface area44800 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)125.830, 125.830, 189.292
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/peptide Ion transport protein / Ion transporter


Mass: 29768.320 Da / Num. of mol.: 1 / Mutation: V100C, Q150C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria)
Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58N2O7S / CHAPS detergent / Comment: detergent *YM
#3: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC (phospholipid) *YM
Has ligand of interestN

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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: 6.29 Å3/Da / Density % sol: 80.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1.8 M ammonium sulfate 0.1 M sodium citrate pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2016
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 16988 / % possible obs: 97.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 54.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.035 / Rrim(I) all: 0.13 / Χ2: 1.125 / Net I/σ(I): 22.06
Reflection shellResolution: 2.89→2.94 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 638 / CC1/2: 0.831 / Rpim(I) all: 0.253 / Rrim(I) all: 0.703 / Χ2: 0.755 / % possible all: 76.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0238refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVY
Resolution: 2.89→44.53 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.046 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.3 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27317 923 5.4 %RANDOM
Rwork0.21421 ---
Obs0.2172 16065 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.234 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å20 Å20 Å2
2--3.42 Å20 Å2
3----6.84 Å2
Refinement stepCycle: 1 / Resolution: 2.89→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 224 0 2201
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0080.0132257
r_bond_other_d0.0010.0172290
r_angle_refined_deg1.5691.6453053
r_angle_other_deg1.141.5445288
r_dihedral_angle_1_deg6.4015241
r_dihedral_angle_2_deg35.52420.87991
r_dihedral_angle_3_deg20.98615347
r_dihedral_angle_4_deg16.3031510
r_chiral_restr0.0690.2310
r_gen_planes_refined0.0060.022223
r_gen_planes_other0.0020.02483
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it6.7437.604967
r_mcbond_other6.737.597966
r_mcangle_it10.04411.4121207
r_mcangle_other10.0411.4221208
r_scbond_it7.2568.4791287
r_scbond_other7.2538.4791288
r_scangle_it
r_scangle_other11.5412.4661846
r_long_range_B_refined14.13592.9372499
r_long_range_B_other14.13592.942500
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.891→2.966 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 46 -
Rwork0.348 914 -
Obs--76.49 %

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