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- PDB-6mwd: NavAb Voltage-gated Sodium Channel, residues 1-239 with mutation T206S -

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Basic information

Entry
Database: PDB / ID: 6mwd
TitleNavAb Voltage-gated Sodium Channel, residues 1-239 with mutation T206S
ComponentsIon transport protein
Keywordsmembrane protein / metal transport / Ion Channel Voltage-gated Sodium Channel
Function / homology
Function and homology information


membrane depolarization during action potential / voltage-gated sodium channel complex / voltage-gated sodium channel activity / identical protein binding / metal ion binding
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
ACETATE ION / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.327 Å
AuthorsLenaeus, M.J. / Catterall, W.A.
CitationJournal: J. Gen. Physiol. / Year: 2019
Title: Molecular dissection of multiphase inactivation of the bacterial sodium channel NaVAb.
Authors: Gamal El-Din, T.M. / Lenaeus, M.J. / Ramanadane, K. / Zheng, N. / Catterall, W.A.
History
DepositionOct 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 20, 2019Group: Database references / Category: pdbx_database_related
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,49110
Polymers29,7751
Non-polymers4,7159
Water50428
1
B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,96340
Polymers119,1014
Non-polymers18,86236
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area34740 Å2
ΔGint-281 kcal/mol
Surface area41170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.495, 124.495, 189.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-2409-

HOH

21B-2423-

HOH

31B-2426-

HOH

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Ion transport protein


Mass: 29775.270 Da / Num. of mol.: 1 / Mutation: T206S
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

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Non-polymers , 5 types, 37 molecules

#2: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 6.17 Å3/Da / Density % sol: 80.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 1.8 Ammonium Sulfate 100 mM Sodium Acetate, pH 5.8

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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 315 / Detector: CCD / Date: Nov 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.327→50 Å / Num. obs: 30943 / % possible obs: 97.3 % / Redundancy: 7 % / Net I/σ(I): 18.3
Reflection shellResolution: 2.327→2.411 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVY

3rvy


Resolution: 2.327→29.572 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.44
RfactorNum. reflection% reflection
Rfree0.2497 1552 5.02 %
Rwork0.2167 --
obs0.2182 30944 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.327→29.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 223 28 2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082182
X-RAY DIFFRACTIONf_angle_d0.9952980
X-RAY DIFFRACTIONf_dihedral_angle_d14.5121218
X-RAY DIFFRACTIONf_chiral_restr0.052365
X-RAY DIFFRACTIONf_plane_restr0.005329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3274-2.40250.33991030.32052067X-RAY DIFFRACTION75
2.4025-2.48830.29371310.29462589X-RAY DIFFRACTION94
2.4883-2.58790.27461400.26752691X-RAY DIFFRACTION98
2.5879-2.70560.27961490.24342713X-RAY DIFFRACTION99
2.7056-2.84810.26521400.222734X-RAY DIFFRACTION100
2.8481-3.02640.23351540.20442726X-RAY DIFFRACTION99
3.0264-3.25980.23661390.20712742X-RAY DIFFRACTION99
3.2598-3.58730.23121440.19532760X-RAY DIFFRACTION99
3.5873-4.10520.21921530.19162729X-RAY DIFFRACTION98
4.1052-5.16770.23451460.20222781X-RAY DIFFRACTION98
5.1677-29.57430.2751530.23272860X-RAY DIFFRACTION97
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)
11.62960.056-0.64214.03833.2746.37080.2639-0.26510.2515-0.2922-0.06660.2246-1.4446-0.5884-0.25410.89320.24840.20220.7482-0.04540.8341-85.8788-30.872-66.3452
20.59560.98611.43847.79897.51047.74-0.8568-0.65680.10180.9210.8261-0.2454-0.5454-1.65090.07462.19130.6263-0.30831.3469-0.13671.092-76.8866-26.9674-82.1201
32.73-0.7251-0.57271.57460.57612.6788-0.0564-0.24960.18230.23380.12840.0367-0.19380.0159-0.12240.5586-0.05150.0010.4826-0.00850.4088-58.0492-47.9684-75.0892
41.9701-0.02780.4312.5589-0.85165.90720.1473-1.20150.25361.26670.06460.343-0.6755-0.0322-0.19550.9111-0.08850.0161.0266-0.09490.6731-55.4763-56.8042-53.8391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1999:2088 )B1999 - 2088
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2089:2096 )B2089 - 2096
3X-RAY DIFFRACTION3( CHAIN B AND RESID 2097:2193 )B2097 - 2193
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2194:2238 )B2194 - 2238

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