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- PDB-5hj8: Bacterial sodium channel neck 3G mutant -

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Basic information

Entry
Database: PDB / ID: 5hj8
TitleBacterial sodium channel neck 3G mutant
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / Voltage gated 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 / MAD / Resolution: 3.7 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 / struct_ncs_dom_lim
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 / _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

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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)69,3175
Polymers69,2774
Non-polymers401
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-117 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.310, 153.350, 165.810
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
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA153 - 27817 - 142
21VALVALBB153 - 27817 - 142
12ARGARGAA153 - 28317 - 147
22ARGARGCC153 - 28317 - 147
13ARGARGAA153 - 28317 - 147
23ARGARGDD153 - 28317 - 147
14VALVALBB150 - 27814 - 142
24VALVALCC150 - 27814 - 142
15VALVALBB150 - 27814 - 142
25VALVALDD150 - 27814 - 142
16GLYGLYCC150 - 28614 - 150
26GLYGLYDD150 - 28614 - 150

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Ion transport protein / sodium channel


Mass: 17319.223 Da / Num. of mol.: 4 / Fragment: UNP residues 143-288 / Mutation: A112G, E113G, D114G
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.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.35 Å3/Da / Density % sol: 80.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 30% PEG400, 20 mM MES, pH 5.4

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 19966 / % possible obs: 99.86 % / Redundancy: 14 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 8.91

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Processing

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

4lto


Resolution: 3.7→15 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / SU B: 120.236 / SU ML: 0.697 / Cross valid method: THROUGHOUT / ESU R: 1.194 / ESU R Free: 0.527 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30409 958 5.1 %RANDOM
Rwork0.27844 ---
obs0.2798 17894 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 299.182 Å2
Baniso -1Baniso -2Baniso -3
1--8.76 Å20 Å20 Å2
2---4.75 Å20 Å2
3---13.5 Å2
Refinement stepCycle: 1 / Resolution: 3.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 1 3 3743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023830
X-RAY DIFFRACTIONr_bond_other_d0.0110.023586
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9455222
X-RAY DIFFRACTIONr_angle_other_deg3.80538131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6315481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02522.955132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.4415562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.144159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024236
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02913
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_it8.41622.5941957
X-RAY DIFFRACTIONr_mcbond_other8.41222.5951956
X-RAY DIFFRACTIONr_mcangle_it14.14733.8462427
X-RAY DIFFRACTIONr_mcangle_other14.14533.8462428
X-RAY DIFFRACTIONr_scbond_it7.24122.8221873
X-RAY DIFFRACTIONr_scbond_other7.23922.8221874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.75734.0292796
X-RAY DIFFRACTIONr_long_range_B_refined29.3394999
X-RAY DIFFRACTIONr_long_range_B_other29.3365000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A62300.09
12B62300.09
21A63150.09
22C63150.09
31A62410.09
32D62410.09
41B61170.1
42C61170.1
51B61110.11
52D61110.11
61C63090.1
62D63090.1
LS refinement shellResolution: 3.7→3.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.515 56 -
Rwork0.485 1274 -
obs--99.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.81571.30050.92662.10821.49311.0780.2468-0.2997-0.00780.3144-0.2767-0.05430.0692-0.30880.02991.86750.0567-0.41951.3899-0.39810.2033166.134523.3616203.4326
20.9961.37071.88841.95172.6933.9837-0.15360.12260.16710.02980.1820.1436-0.16240.4183-0.02841.1268-0.0348-0.26541.1455-0.33230.4935176.559422.427188.0258
31.43520.40940.43560.1360.10380.1625-0.2437-0.1556-0.00810.02270.1326-0.0572-0.3075-0.10490.11121.8625-0.119-0.28471.3467-0.3590.1576168.085237.388182.3811
43.86293.95963.56314.06913.64883.4050.2906-0.2848-0.1220.3559-0.223-0.18280.305-0.1599-0.06761.34750.0225-0.38050.9041-0.49850.5622156.633537.388196.1567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A150 - 284
2X-RAY DIFFRACTION2B150 - 279
3X-RAY DIFFRACTION3C150 - 286
4X-RAY DIFFRACTION4D150 - 286

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