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- PDB-4ltq: Bacterial sodium channel in low calcium, P42 space group -

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Basic information

Entry
Database: PDB / ID: 4ltq
TitleBacterial sodium channel in low calcium, P42 space group
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / cation channel fold / coiled coil sodium channel / plasma membrane
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 / MOLECULAR REPLACEMENT / Resolution: 5.5 Å
AuthorsShaya, D. / Findeisen, F. / Abderemane-Ali, F. / Arrigoni, C. / Wong, S. / Reddy Nurva, S. / Loussouarn, G. / Minor, D.L.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels.
Authors: Shaya, D. / Findeisen, F. / Abderemane-Ali, F. / Arrigoni, C. / Wong, S. / Nurva, S.R. / Loussouarn, G. / Minor, D.L.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Sep 20, 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
H: Ion transport protein
I: Ion transport protein
J: Ion transport protein
K: Ion transport protein


Theoretical massNumber of molelcules
Total (without water)139,7078
Polymers139,7078
Non-polymers00
Water00
1
A: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein


Theoretical massNumber of molelcules
Total (without water)69,8534
Polymers69,8534
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-124 kcal/mol
Surface area26230 Å2
MethodPISA
2
H: Ion transport protein
I: Ion transport protein
J: Ion transport protein
K: Ion transport protein


Theoretical massNumber of molelcules
Total (without water)69,8534
Polymers69,8534
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-124 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.136, 181.136, 94.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51H
61I
71J
81K

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 150 - 285 / Label seq-ID: 14 - 149

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5HE
6IF
7JG
8KH

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.990474, 0.032616, 0.133781), (-0.134477, 0.020174, 0.990711), (0.029614, -0.999264, 0.024368)-5.3587, 127.70514, 144.15157
3given(0.980359, -0.099432, 0.170322), (-0.105395, -0.994082, 0.02631), (0.166698, -0.043745, -0.985037)12.82047, 273.88129, 19.46816
4given(0.990034, -0.138428, 0.025902), (0.02439, -0.012611, -0.999623), (0.138702, 0.990292, -0.009109)19.30301, 146.73317, -129.46487
5given(-0.058316, -0.970754, -0.232887), (0.981113, -0.012632, -0.193023), (0.184436, -0.239745, 0.953156)278.50809, 101.72891, 3.20003
6given(-0.000131, -0.994056, -0.108866), (0.209271, -0.106483, 0.972043), (-0.977858, -0.022655, 0.208041)274.19757, 95.3769, 50.98726
7given(-0.122557, -0.991445, -0.044897), (-0.965247, 0.108553, 0.237729), (-0.230821, 0.072472, -0.970293)276.19379, 143.72261, 58.63654
8given(-0.188123, -0.966013, -0.177281), (-0.197151, 0.213973, -0.956738), (0.962154, -0.145033, -0.230704)281.01828, 149.41412, 9.80708

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Components

#1: Protein
Ion transport protein / sodium channel


Mass: 17463.344 Da / Num. of mol.: 8
Fragment: Pore and cytoplasmic domains (UNP residues 143-288)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkalilimnicola ehrlichii (bacteria) / Gene: Mlg_0322 / Plasmid: pet24b HM3C-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q0ABW0

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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: 5.52 Å3/Da / Density % sol: 77.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM magnesium chloride, 30% PEG400, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2010
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.598
11-H, K, -L20.402
ReflectionResolution: 5.5→50 Å / Num. all: 10095 / Num. obs: 9811 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 307 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.8
Reflection shellResolution: 5.5→5.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.916 / Mean I/σ(I) obs: 0.7 / Num. unique all: 1236 / % possible all: 86.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LTO

4lto


Resolution: 5.5→15 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.918 / SU B: 45.904 / SU ML: 0.526 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29412 426 4.6 %RANDOM
Rwork0.26649 ---
all0.26759 9289 --
obs0.26759 8863 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 292.6 Å2
Baniso -1Baniso -2Baniso -3
1--15.17 Å2-0 Å2-0 Å2
2---15.17 Å2-0 Å2
3---30.33 Å2
Refinement stepCycle: LAST / Resolution: 5.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8086 0 0 0 8086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.93411378
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61151080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.81922.815270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.105151132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7171516
X-RAY DIFFRACTIONr_chiral_restr0.0630.21370
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026140
X-RAY DIFFRACTIONr_gen_planes_other
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_it37.58376.1114344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it55.5455416
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it49.42381.0913960
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined69.81912988
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 996 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A36.44
2B39.6
3C37.72
4D38.84
5H36.97
6I38.21
7J38.48
8K35.78
LS refinement shellResolution: 5.5→5.625 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 15 -
Rwork0.173 437 -
obs-437 71.63 %

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