[English] 日本語
Yorodumi
- PDB-6p6x: Crystal structure of voltage-gated sodium channel NavAb G94C/Q150... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p6x
TitleCrystal structure of voltage-gated sodium channel NavAb G94C/Q150C mutant in the activated state
ComponentsIon transport proteinIon transporter
Keywordsmembrane protein / metal transport / Ion channel / ion transport protein
Function / homologyIon transport domain / Voltage-dependent channel domain superfamily / Ion transport protein / ion channel activity / integral component of membrane / identical protein binding / Ion transport protein
Function and homology information
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWisedchaisri, G. / Tonggu, L. / McCord, E. / Gamal El-Din, T.M. / Wang, L. / Zheng, N. / Catterall, W.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and StrokeR01 NS015751 United States
National Institutes of Health/National Heart, Lung, and Blood InstituteR01 HL112808 United States
National Institutes of Health/National Institute of General Medical SciencesT32 GM007750 United States
Howard Hughes Medical Institute United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,15112
Polymers29,8101
Non-polymers7,34011
Water0
1
A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,60248
Polymers119,2424
Non-polymers29,36144
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area50300 Å2
ΔGint-320 kcal/mol
Surface area39240 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)124.449, 124.449, 193.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein/peptide Ion transport protein / Ion transporter


Mass: 29810.398 Da / Num. of mol.: 1 / Mutation: G94C, Q150C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria)
Strain: RM4018 / Gene: Abu_1752 / Variant: RM4018 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC (phospholipid) *YM
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58N2O7S / CHAPS detergent / Comment: detergent *YM
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 6.28 Å3/Da / Density % sol: 80.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.8 M ammonium sulfate 0.1 M sodium citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2018
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 19146 / % possible obs: 94.8 % / Redundancy: 19.6 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.026 / Rrim(I) all: 0.12 / Χ2: 0.962 / Net I/σ(I): 27.75
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 556 / CC1/2: 0.63 / Rpim(I) all: 0.375 / Χ2: 0.878 / % possible all: 56.3

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0238refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVY
Resolution: 2.75→44.04 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.861 / SU B: 8.8 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.292 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26543 851 5.1 %RANDOM
Rwork0.21321 ---
Obs0.21579 15906 83.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.75→44.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 342 0 2159
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0110.0132213
r_bond_other_d0.0010.0172309
r_angle_refined_deg1.7411.6632972
r_angle_other_deg1.1821.5415338
r_dihedral_angle_1_deg6.8845228
r_dihedral_angle_2_deg32.142078
r_dihedral_angle_3_deg20.7115307
r_dihedral_angle_4_deg20.1251510
r_chiral_restr0.0770.2302
r_gen_planes_refined0.0080.022080
r_gen_planes_other0.0020.02450
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it3.7983.754912
r_mcbond_other3.7883.749911
r_mcangle_it5.8625.6131137
r_mcangle_other5.865.621138
r_scbond_it4.5974.921300
r_scbond_other4.5964.9231301
r_scangle_it
r_scangle_other7.347.171835
r_long_range_B_refined9.47848.2062380
r_long_range_B_other9.47648.2372381
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.751→2.823 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 9 -
Rwork0.269 208 -
Obs--14.83 %

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more