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- PDB-4ltp: Bacterial sodium channel in high calcium, I222 space group, crystal 2 -

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Basic information

Entry
Database: PDB / ID: 4ltp
TitleBacterial sodium channel in high calcium, I222 space group, crystal 2
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / cation channel fold / coiled coil sodium channel / plasma membrane
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ion transport protein
Similarity search - Component
Biological speciesAlkalilimnicola ehrlichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,13411
Polymers69,8534
Non-polymers2817
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-145 kcal/mol
Surface area26400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.265, 161.499, 161.690
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(0.22084, 0.374525, 0.900533), (-0.918153, 0.391277, 0.062431), (-0.328976, -0.840615, 0.430281)-46.32777, -58.43068, -23.10557
3given(-0.590003, -0.536184, 0.603658), (-0.576133, -0.244216, -0.780019), (0.565656, -0.808001, -0.164825)-99.43748, -39.8119, 32.2779
4given(0.191704, -0.930662, -0.311636), (0.359926, 0.362068, -0.859861), (0.913073, 0.052673, 0.404379)-52.873, 19.80334, 56.85528

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Components

#1: Protein
Ion transport protein / sodium channel


Mass: 17463.344 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 6.88 Å3/Da / Density % sol: 82.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 200 mM calcium chloride, 30% PEG400, 100 mM sodium acetate, pH 5.0, 0.5 M TMAO, 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: Nov 21, 2011
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
ReflectionResolution: 3.8→50 Å / Num. all: 19278 / Num. obs: 19162 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 143 Å2 / Rmerge(I) obs: 0.181 / Net I/σ(I): 6
Reflection shellResolution: 3.8→4.01 Å / Redundancy: 6.4 % / Rmerge(I) obs: 3.306 / Mean I/σ(I) obs: 0.5 / Num. unique all: 2683 / % possible all: 97

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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: 3.8→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.95 / SU B: 37.039 / SU ML: 0.478 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 1.378 / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27289 962 5.1 %RANDOM
Rwork0.22469 ---
all0.22708 18975 --
obs0.22708 18013 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 170.143 Å2
Baniso -1Baniso -2Baniso -3
1-10.06 Å2-0 Å20 Å2
2---0.35 Å20 Å2
3----9.71 Å2
Refinement stepCycle: LAST / Resolution: 3.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 7 4 4090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024192
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9355743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5295548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41622.782133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.19515564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.362158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023092
X-RAY DIFFRACTIONr_mcbond_it15.00818.6532204
X-RAY DIFFRACTIONr_mcangle_it23.28827.9332748
X-RAY DIFFRACTIONr_scbond_it17.87719.0811988
X-RAY DIFFRACTIONr_long_range_B_refined32.5327302
Refine LS restraints NCS

Ens-ID: 1 / Number: 996 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 3

Dom-IDAuth asym-IDRms dev position (Å)
1A18.97
2B22.45
3C18.44
4D20.39
LS refinement shellResolution: 3.8→3.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 55 -
Rwork0.432 1051 -
obs-1051 83.85 %

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