[English] 日本語
Yorodumi
- PDB-5ebm: KcsA T75G mutant in the nonconductive state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ebm
TitleKcsA T75G mutant in the nonconductive state
Components
  • (Antibody Fab Fragment Light ...) x 2
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / alpha-helical / Fab / Channel
Function / homology
Function and homology information


monoatomic ion transmembrane transport / identical protein binding / plasma membrane
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 / NONAN-1-OL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
Model detailsmutant1
AuthorsMatulef, K. / Valiyaveetil, F.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2016
Title: Individual Ion Binding Sites in the K(+) Channel Play Distinct Roles in C-type Inactivation and in Recovery from Inactivation.
Authors: Matulef, K. / Annen, A.W. / Nix, J.C. / Valiyaveetil, F.I.
History
DepositionOct 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_symmetry / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antibody Fab Fragment Light Chain
B: Antibody Fab Fragment Light Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9438
Polymers60,0573
Non-polymers8875
Water1,31573
1
A: Antibody Fab Fragment Light Chain
B: Antibody Fab Fragment Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Fab Fragment Light Chain
B: Antibody Fab Fragment Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Fab Fragment Light Chain
B: Antibody Fab Fragment Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Fab Fragment Light Chain
B: Antibody Fab Fragment Light Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,77332
Polymers240,22612
Non-polymers3,54620
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_595-x,-y+4,z1
crystal symmetry operation3_775-y+2,x+2,z1
crystal symmetry operation4_375y-2,-x+2,z1
Unit cell
Length a, b, c (Å)155.720, 155.720, 75.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-1003-

K

21C-1004-

K

31C-1005-

K

-
Components

-
Protein , 1 types, 1 molecules C

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


Mass: 13324.719 Da / Num. of mol.: 1 / Fragment: UNP residues 1-125 / Mutation: T75G
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 Light Chain


Mass: 23296.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#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 line (production host): Hybridoma / Production host: Mus musculus (house mouse)

-
Non-polymers , 4 types, 78 molecules

#4: Chemical ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#5: Chemical ChemComp-F09 / NONAN-1-OL / 1-Nonanol


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 400

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→55.054 Å / Num. all: 31464 / Num. obs: 31464 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 50.26 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Rsym value: 0.085 / Net I/av σ(I): 8.287 / Net I/σ(I): 15.6 / Num. measured all: 219611
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.646.21.1240.72831745630.4931.1241.5100
2.64-2.87.20.7191.13098543300.290.7192.5100
2.8-2.996.80.4011.92770740730.1670.4014.5100
2.99-3.236.70.2093.72557337960.0870.2098.5100
3.23-3.547.20.1226.32496334740.0490.12215100
3.54-3.957.30.089.32312131580.0320.0822.5100
3.95-4.567.40.051142055327900.020.05133.5100
4.56-5.597.30.04415.91747923870.0170.04436.9100
5.59-7.917.30.042161350818480.0170.04235.1100
7.91-55.0547.10.02722.1740510450.0110.02751.499.4

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4C

1k4c


Resolution: 2.5→42.783 Å / FOM work R set: 0.7901 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 2991 10.14 %
Rwork0.2158 26505 -
obs0.2194 29496 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.61 Å2 / Biso mean: 31.26 Å2 / Biso min: 3.83 Å2
Refinement stepCycle: final / Resolution: 2.5→42.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 0 44 73 4098
Biso mean--82.02 25.69 -
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034082
X-RAY DIFFRACTIONf_angle_d0.5825574
X-RAY DIFFRACTIONf_chiral_restr0.04644
X-RAY DIFFRACTIONf_plane_restr0.003706
X-RAY DIFFRACTIONf_dihedral_angle_d9.7391410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.54110.39831180.33651022114076
2.5411-2.58490.39081370.32321091122883
2.5849-2.63190.32241200.29661122124284
2.6319-2.68250.37271260.2881167129387
2.6825-2.73730.37941390.28391170130988
2.7373-2.79680.31921270.27561197132490
2.7968-2.86180.31231480.25891218136692
2.8618-2.93340.27941480.2621239138792
2.9334-3.01270.29671310.26391266139793
3.0127-3.10130.34521430.24931263140696
3.1013-3.20140.2911280.24241324145297
3.2014-3.31580.28531590.24991301146097
3.3158-3.44850.27361460.22721317146398
3.4485-3.60530.22121460.22461338148499
3.6053-3.79530.23251640.20991297146199
3.7953-4.03290.25661340.2011377151199
4.0329-4.3440.23261660.193313161482100
4.344-4.78070.22451490.171813571506100
4.7807-5.47120.19641380.175213681506100
5.4712-6.88850.22021810.186413571538100
6.8885-42.78960.19611430.20041398154199

+
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://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