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- PDB-5iwo: Bacterial sodium channel pore domain, low bromide -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5iwo
TitleBacterial sodium channel pore domain, low bromide
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / bacterial sodium channel / high Br
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
BROMIDE ION / Ion transport protein
Similarity search - Component
Biological speciesAlkalilimnicola ehrlichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsShaya, D. / Findeisen, F. / Rohaim, 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
DepositionMar 22, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionMar 30, 2016ID: 5HKU
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9335
Polymers69,8534
Non-polymers801
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13430 Å2
ΔGint-103 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.720, 159.950, 168.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Ion transport protein


Mass: 17463.344 Da / Num. of mol.: 4 / Fragment: UNP residues 143-288
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: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br

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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: 7.32 Å3/Da / Density % sol: 83.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.9 / Details: 28% PEG300, 100 mM sodium acetate, pH 4.9

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.33→62.49 Å / Num. obs: 29811 / % possible obs: 98.6 % / Redundancy: 8.5 % / Rsym value: 0.23 / Net I/σ(I): 8.7
Reflection shellResolution: 3.33→3.45 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LTO

4lto


Resolution: 3.33→15 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / ESU R: 0.472 / ESU R Free: 0.356
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1534 5.1 %RANDOM
Rwork0.209 ---
obs0.212 28277 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 112.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.69 Å20 Å20 Å2
2---4.93 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 3.33→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 1 0 4495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONBOND LENGTHS REFINED ATOMS0.0130.0194625
X-RAY DIFFRACTIONBOND ANGLES REFINED ATOMS1.791.9336282
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD 17.3435551
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD 235.87422.683205
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD 325.73815769
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD 422.0781531
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS0.1140.2701
X-RAY DIFFRACTIONGENERAL PLANES REFINED ATOMS0.0070.023443
LS refinement shellResolution: 3.33→3.412 Å
RfactorNum. reflection% reflection
Rfree0.408 92 5 %
Rwork0.374 1858 -
obs--98.39 %

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