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- PDB-5hk6: Bacterial sodium channel neck 3G mutant, SAD -

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Basic information

Entry
Database: PDB / ID: 5hk6
TitleBacterial sodium channel neck 3G mutant, SAD
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / Bacterial voltage gated sodium channel
Function / homologyVoltage-gated cation channel calcium and sodium / voltage-gated sodium channel complex / voltage-gated sodium channel activity / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / metal ion binding / identical protein binding / Ion transport protein
Function and homology information
Biological speciesAlkalilimnicola ehrlichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 5.5 Å
AuthorsRohaim, A. / Minor, D.L.
CitationJournal: Cell / Year: 2016
Title: Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation.
Authors: Arrigoni, C. / Rohaim, A. / Shaya, D. / Findeisen, F. / Stein, R.A. / Nurva, S.R. / Mishra, S. / Mchaourab, H.S. / Minor, D.L.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)70,4024
Polymers70,4024
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-108 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.350, 150.190, 167.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A153 - 278
2010B153 - 278
1020A153 - 283
2020C153 - 283
1030A153 - 283
2030D153 - 283
1040B150 - 278
2040C150 - 278
1050B150 - 278
2050D150 - 278
1060C150 - 286
2060D150 - 286

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Ion transport protein / sodium channel


Mass: 17600.592 Da / Num. of mol.: 4 / Fragment: UNP residues 143-288 / Mutation: A112G, E113G, D114G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkalilimnicola ehrlichii (bacteria) / Gene: Mlg_0322 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0ABW0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 6.44 Å3/Da / Density % sol: 80.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 30% PEG400, 100 mM MES, pH 6.6

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 5.5→50 Å / Num. all: 5848 / Num. obs: 5848 / % possible obs: 99.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 5.5→15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.943 / SU B: 394.502 / SU ML: 1.654 / Cross valid method: THROUGHOUT / ESU R Free: 1.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26423 297 5.1 %RANDOM
Rwork0.25574 ---
obs0.25618 5551 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 280.736 Å2
Baniso -1Baniso -2Baniso -3
1-31.05 Å20 Å20 Å2
2---24.6 Å20 Å2
3----6.45 Å2
Refinement stepCycle: LAST / Resolution: 5.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3697 0 0 4 3701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023836
X-RAY DIFFRACTIONr_bond_other_d00.023590
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.9655230
X-RAY DIFFRACTIONr_angle_other_deg3.95838139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.665483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80322.901131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.19515487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.919159
X-RAY DIFFRACTIONr_chiral_restr0.1240.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024248
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02917
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it20.74625.0871965
X-RAY DIFFRACTIONr_mcbond_other20.72325.0931964
X-RAY DIFFRACTIONr_mcangle_it34.5437.4482437
X-RAY DIFFRACTIONr_mcangle_other34.53937.4482438
X-RAY DIFFRACTIONr_scbond_it20.06426.3161871
X-RAY DIFFRACTIONr_scbond_other20.05926.3141872
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other34.25839.0242794
X-RAY DIFFRACTIONr_long_range_B_refined50.2694598
X-RAY DIFFRACTIONr_long_range_B_other50.2664599
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A59690.08
12B59690.08
21A61420.07
22C61420.07
31A60050.09
32D60050.09
41B60510.06
42C60510.06
51B59600.08
52D59600.08
61C62160.08
62D62160.08
LS refinement shellResolution: 5.5→5.623 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 24 -
Rwork0.364 375 -
obs--100 %
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)
11.59241.05821.86150.80071.0482.6438-0.23840.08250.2419-0.22770.09270.159-0.15620.14950.14570.22210.0305-0.00670.3377-0.15040.233173.166223.0556205.1975
20.2211-0.00860.11310.1186-0.29970.8379-0.19410.04160.3576-0.0339-0.0056-0.0127-0.0619-0.05330.19970.30580.0486-0.3290.2904-0.00820.5993183.001121.4806189.5402
31.12731.5541.60852.29362.27882.37970.0236-0.10770.14170.0423-0.17420.0632-0.0626-0.06790.15060.2248-0.0913-0.00690.28870.00570.137175.000537.0351184.33
41.87270.22191.37950.6461-0.75862.40440.4369-1.1733-0.38980.0522-0.1288-0.15780.454-1.0374-0.30810.5642-0.1154-0.2370.92620.0880.3409163.435537.0013197.9408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A149 - 284
2X-RAY DIFFRACTION2B153 - 279
3X-RAY DIFFRACTION3C153 - 286
4X-RAY DIFFRACTION4D153 - 286

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