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- PDB-4j7c: KtrAB potassium transporter from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 4j7c
TitleKtrAB potassium transporter from Bacillus subtilis
Components
  • Ktr system potassium uptake protein A
  • Ktr system potassium uptake protein B
KeywordsTRANSPORT PROTEIN / KtrB pore-forming membrane protein / KtrA regulatory cytosolic ring / Potassium ion transport / Potassium / cell membrane / cytosol
Function / homology
Function and homology information


potassium:chloride symporter activity / monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
TrkH potassium transport family / Cation transporter / Cation transport protein / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain ...TrkH potassium transport family / Cation transporter / Cation transport protein / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Ktr system potassium uptake protein A / Ktr system potassium uptake protein B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsVieira-Pires, R.S. / Morais-Cabral, J.H.
CitationJournal: Nature / Year: 2013
Title: The structure of the KtrAB potassium transporter
Authors: Vieira-Pires, R.S. / Szollosi, A. / Morais-Cabral, J.H.
History
DepositionFeb 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 8, 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_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
I: Ktr system potassium uptake protein B
J: Ktr system potassium uptake protein B
K: Ktr system potassium uptake protein B
L: Ktr system potassium uptake protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,08724
Polymers401,87412
Non-polymers4,21412
Water0
1
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
I: Ktr system potassium uptake protein B
J: Ktr system potassium uptake protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,72320
Polymers300,58810
Non-polymers4,13610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
K: Ktr system potassium uptake protein B
L: Ktr system potassium uptake protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,72320
Polymers300,58810
Non-polymers4,13610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53580 Å2
ΔGint-318 kcal/mol
Surface area136910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.520, 140.190, 153.930
Angle α, β, γ (deg.)90.00, 105.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12I
22J
32K
42L

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSMETMETAA7 - 2227 - 222
21LYSLYSMETMETBB7 - 2227 - 222
31LYSLYSMETMETCC7 - 2227 - 222
41LYSLYSMETMETDD7 - 2227 - 222
51LYSLYSMETMETEE7 - 2227 - 222
61LYSLYSMETMETFF7 - 2227 - 222
71LYSLYSMETMETGG7 - 2227 - 222
81LYSLYSMETMETHH7 - 2227 - 222
12PROPROGLYGLYII16 - 44536 - 465
22PROPROGLYGLYJJ16 - 44536 - 465
32PROPROGLYGLYKK16 - 44536 - 465
42PROPROGLYGLYLL16 - 44536 - 465

NCS ensembles :
ID
1
2
DetailsTHE KNOWN BIOLOGICAL RELEVANT ASSEMBLY IS ONE OCTAMER BOUND TO ONE DIMER, THEREFORE EITHER "CHAINS: A, B, C, D, E, F, G, H, AND CHAINS: I,J" OR "CHAINS: A, B, C, D, E, F, G, H, AND CHAINS: K,L".

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Components

#1: Protein
Ktr system potassium uptake protein A / K(+)-uptake protein KtrA


Mass: 24912.748 Da / Num. of mol.: 8 / Mutation: C22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ktrA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32080
#2: Protein
Ktr system potassium uptake protein B / K(+)-uptake protein KtrB


Mass: 50642.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ktrB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32081
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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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: 3.79 Å3/Da / Density % sol: 67.52 % / Mosaicity: 0 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M (N-(2-Acetamido)-iminodiacetic acid) buffer, 20% polyethylene glycol 400, 0.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.3→148.186 Å / Num. all: 90089 / Num. obs: 87633 / % possible obs: 97.2 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 2.3 % / Rsym value: 0.163 / Net I/σ(I): 5.3
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.3-3.482.11.7550.627187126931.111.7551.3470.696.7
3.48-3.692.21.0780.926526121100.6791.0780.8291.197.6
3.69-3.942.30.7041.425576113620.4410.7040.5441.697.5
3.94-4.262.30.3862.624499106480.240.3860.2992.997.8
4.26-4.672.30.2294.32285197580.1410.2290.1784.897.6
4.67-5.222.40.1875.22100488700.1150.1870.146697.7
5.22-6.022.40.1885.21843577670.1160.1880.1476.197.3
6.02-7.382.40.1375.51568166130.0850.1370.1078.397.2
7.38-10.442.40.04420.71202350870.0270.0440.03420.796.5
10.44-55.0032.30.02922.8631527250.0180.0290.02231.393.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PJZ, 2HMW

3pjz

2hmw


Resolution: 3.5→147.44 Å / Cor.coef. Fo:Fc: 0.832 / Cor.coef. Fo:Fc free: 0.834 / WRfactor Rfree: 0.2367 / WRfactor Rwork: 0.2286 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8092 / SU B: 34.155 / SU ML: 0.521 / SU Rfree: 0.7153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.715 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 3061 5.1 %RANDOM
Rwork0.258 ---
all0.2588 60372 --
obs0.2588 60372 79.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200 Å2 / Biso mean: 66.3195 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-0.32 Å2
2---2.82 Å20 Å2
3---3.52 Å2
Refinement stepCycle: LAST / Resolution: 3.5→147.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26744 0 252 0 26996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227048
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.97736781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36153432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76224.3571003
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.213154579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6371597
X-RAY DIFFRACTIONr_chiral_restr0.1120.24490
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119505
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A15919.31
12B159111.1
13C159118.95
14D159114.58
15E159114.12
16F15918.91
17G159115.39
18H159113.25
21I32206.94
22J32207.33
23K32208.52
24L32207.02
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 55 -
Rwork0.302 1014 -
all-1069 -
obs--19.36 %

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