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- PDB-4ltr: Bacterial sodium channel, His245Gly mutant, I222 space group -

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Basic information

Entry
Database: PDB / ID: 4ltr
TitleBacterial sodium channel, His245Gly mutant, I222 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: 5.8 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


Theoretical massNumber of molelcules
Total (without water)69,5294
Polymers69,5294
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-121 kcal/mol
Surface area26510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.205, 161.384, 165.449
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
31C
41D

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.290504, 0.283711, 0.913847), (-0.907794, 0.383652, 0.169473), (-0.302518, -0.878817, 0.369003)-171.03464, 27.22528, 178.39412
3given(-0.450781, -0.616359, 0.645676), (-0.660624, -0.256096, -0.705685), (0.60031, -0.744658, -0.291739)-48.7536, 223.74321, 272.72321
4given(0.267838, -0.919702, -0.287072), (0.267872, 0.357295, -0.894754), (0.925477, 0.16275, 0.34206)126.88696, 199.82185, 91.60007

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Components

#1: Protein
Ion transport protein / sodium channel


Mass: 17382.250 Da / Num. of mol.: 4
Fragment: Pore and cytoplasmic domains (UNP residues 143-288)
Mutation: H245G
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: 7.55 Å3/Da / Density % sol: 83.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 28% PEG400, 100 mM sodium acetate, pH 4.5, 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: 1.70192 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2013
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.70192 Å / Relative weight: 1
ReflectionResolution: 5.8→50 Å / Num. all: 6057 / Num. obs: 5978 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 305 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 0.7
Reflection shellResolution: 5.8→6.11 Å / Redundancy: 13.6 % / Rmerge(I) obs: 4.181 / Mean I/σ(I) obs: 0.7 / Num. unique all: 844 / % possible all: 98.7

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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: 5.8→15 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.89 / SU B: 156.651 / SU ML: 1.535 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 1.593 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.31762 292 4.9 %RANDOM
Rwork0.26244 ---
all0.26519 5976 --
obs0.26519 5684 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 308.045 Å2
Baniso -1Baniso -2Baniso -3
1-13.56 Å20 Å2-0 Å2
2---37.37 Å2-0 Å2
3---23.81 Å2
Refinement stepCycle: LAST / Resolution: 5.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 0 0 4034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024152
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9661.9345689
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3665540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64622.815135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.39215566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.36158
X-RAY DIFFRACTIONr_chiral_restr0.060.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023070
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_it42.91692.3062172
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it67.1652708
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it49.29790.6691980
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined84.0756545
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)
1A53.5
2B57.36
3C59.08
4D58.65
LS refinement shellResolution: 5.8→5.927 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.576 17 -
Rwork0.549 345 -
obs-345 97.57 %

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