[English] 日本語
Yorodumi
- PDB-4msw: Y78 ester mutant of KcsA in high K+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4msw
TitleY78 ester mutant of KcsA in high K+
Components
  • (ANTIBODY FAB FRAGMENT ...) x 2
  • pH-gated potassium channel KcsA
KeywordsTRANSPORT PROTEIN / Membrane protein / Channel / Ester / Unnatural amino acid
Function / homology
Function and homology information


delayed rectifier potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DIACYL GLYCEROL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsMatulef, K. / Valiyaveetil, F.I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Using protein backbone mutagenesis to dissect the link between ion occupancy and C-type inactivation in K+ channels.
Authors: Matulef, K. / Komarov, A.G. / Costantino, C.A. / Valiyaveetil, F.I.
History
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANTIBODY FAB FRAGMENT HEAVY CHAIN
B: ANTIBODY FAB FRAGMENT LIGHT CHAIN
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,69610
Polymers57,8373
Non-polymers8607
Water4,666259
1
A: ANTIBODY FAB FRAGMENT HEAVY CHAIN
B: ANTIBODY FAB FRAGMENT LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,8472
Polymers46,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-23 kcal/mol
Surface area19350 Å2
MethodPISA
2
C: pH-gated potassium channel KcsA
hetero molecules

C: pH-gated potassium channel KcsA
hetero molecules

C: pH-gated potassium channel KcsA
hetero molecules

C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,39732
Polymers43,9594
Non-polymers3,43828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area10750 Å2
ΔGint-99 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.530, 154.530, 75.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-1002-

K

21C-1003-

K

31C-1004-

K

41C-1005-

K

51C-1006-

K

61C-1007-

K

71C-1127-

HOH

-
Components

-
Protein , 1 types, 1 molecules C

#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 10989.735 Da / Num. of mol.: 1 / Fragment: UNP residues 22-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334

-
Antibody , 2 types, 2 molecules AB

#1: Antibody ANTIBODY FAB FRAGMENT HEAVY CHAIN


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: Hybridoma / Production host: Komagataella pastoris (fungus)
#2: Antibody ANTIBODY FAB FRAGMENT LIGHT CHAIN


Mass: 23435.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: Hybridoma / Production host: Komagataella pastoris (fungus)

-
Non-polymers , 3 types, 266 molecules

#4: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHERE IS AN ESTER LINKAGE BETWEEN RESIDUES 77 AND 78 OF CHAIN C RATHER THAN A PEPTIDE BACKBONE LINKAGE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PEG400, Magnesium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
PH range: 5.75-6.0

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.06→42 Å / Num. obs: 54941 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 32.53 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.029 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.06-2.14.70.56626651.057197.2
2.1-2.135.30.47726611.04199.3
2.13-2.176.10.47227640.996199.9
2.17-2.226.60.4527291.0191100
2.22-2.2770.49727431.0741100
2.27-2.327.30.38427490.981100
2.32-2.387.50.34827281.0641100
2.38-2.447.60.31627461.081100
2.44-2.517.60.25427601.0331100
2.51-2.67.60.2227271.041100
2.6-2.697.60.17827641.021100
2.69-2.87.60.14327221.0011100
2.8-2.927.60.11627611.0261100
2.92-3.087.60.09327441.0561100
3.08-3.277.60.08127560.9721100
3.27-3.527.60.06527851.0191100
3.52-3.887.60.05427521.0121100
3.88-4.447.60.04727680.9641100
4.44-5.597.60.04927801.042199.9
5.59-427.40.03928371.089199.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→36.423 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8294 / SU ML: 0.22 / σ(F): 0 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 5253 10.02 %
Rwork0.1961 --
obs0.1994 52404 95.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.66 Å2 / Biso mean: 37.6849 Å2 / Biso min: 10.18 Å2
Refinement stepCycle: LAST / Resolution: 2.06→36.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 37 259 4353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074162
X-RAY DIFFRACTIONf_angle_d1.055678
X-RAY DIFFRACTIONf_chiral_restr0.069649
X-RAY DIFFRACTIONf_plane_restr0.004719
X-RAY DIFFRACTIONf_dihedral_angle_d12.4351455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.06-2.08610.33751710.3031281145282
2.0861-2.11060.29491580.25671383154183
2.1106-2.13640.29151500.24951416156687
2.1364-2.16340.29731620.23161494165689
2.1634-2.19190.31181520.24171483163590
2.1919-2.22190.23631430.22931536167992
2.2219-2.25360.28781690.22611499166890
2.2536-2.28730.27731570.21661489164691
2.2873-2.3230.24771700.20481543171393
2.323-2.36110.22671590.20671580173995
2.3611-2.40180.24591800.20471522170295
2.4018-2.44540.25371710.21021560173194
2.4454-2.49250.26291800.19111567174796
2.4925-2.54330.24771760.21011598177497
2.5433-2.59860.25071920.19851554174696
2.5986-2.6590.23281740.20371597177197
2.659-2.72550.25651860.20191604179097
2.7255-2.79920.2381840.20971597178198
2.7992-2.88150.23921860.20761630181698
2.8815-2.97450.27551770.21761653183099
2.9745-3.08070.23311850.21071600178599
3.0807-3.2040.26361690.1991673184299
3.204-3.34980.21711850.198716311816100
3.3498-3.52620.21741820.189716691851100
3.5262-3.74690.20812070.188916241831100
3.7469-4.03590.20051590.182816761835100
4.0359-4.44140.19752070.171316411848100
4.4414-5.08260.2021740.164416871861100
5.0826-6.39790.21421980.185416691867100
6.3979-36.42870.20881900.19251695188599

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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