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- PDB-5hkd: Bacterial sodium channel neck 7G mutant -

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Basic information

Entry
Database: PDB / ID: 5hkd
TitleBacterial sodium channel neck 7G mutant
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / Bacterial sodium channel
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
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 1.1Sep 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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_conn.ptnr2_label_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)68,3475
Polymers68,3074
Non-polymers401
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-111 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.100, 137.990, 173.160
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 / sodium channel


Mass: 17076.822 Da / Num. of mol.: 4 / Fragment: UNP residues 143-288 / Mutation: A112G, E113G, D114G, A115G, K116G, R117G, I118G
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 5.99 Å3/Da / Density % sol: 79.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 30% PEG400, 20 mM MES, pH 5.8

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315r / 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.8→68.6 Å / Num. obs: 18097 / % possible obs: 97.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.66 / Net I/σ(I): 6.22
Reflection shellHighest resolution: 3.8 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LTO

4lto


Resolution: 3.8→15 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / ESU R: 4.035 / ESU R Free: 0.606
RfactorNum. reflection% reflectionSelection details
Rfree0.31198 795 5 %RANDOM
Rwork0.2727 ---
obs0.27467 15088 96.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 162.235 Å2
Baniso -1Baniso -2Baniso -3
1--11.36 Å20 Å20 Å2
2--5.12 Å20 Å2
3---6.24 Å2
Refinement stepCycle: 1 / Resolution: 3.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 1 2 3697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023804
X-RAY DIFFRACTIONr_bond_other_d00.023561
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9395196
X-RAY DIFFRACTIONr_angle_other_deg3.91838067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6335477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02422.558129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.35615551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.007159
X-RAY DIFFRACTIONr_chiral_restr0.0950.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024212
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02925
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_it15.36316.4531932
X-RAY DIFFRACTIONr_mcbond_other15.3216.4571931
X-RAY DIFFRACTIONr_mcangle_it24.78424.5752401
X-RAY DIFFRACTIONr_mcangle_other24.78324.5762402
X-RAY DIFFRACTIONr_scbond_it14.71217.3781872
X-RAY DIFFRACTIONr_scbond_other14.70817.3771873
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other24.30525.6472796
X-RAY DIFFRACTIONr_long_range_B_refined32.9944861
X-RAY DIFFRACTIONr_long_range_B_other32.9914862
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.8→3.892 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 53 -
Rwork0.447 1057 -
obs--98.58 %

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