[English] 日本語
Yorodumi
- PDB-6s5b: Non-square conformation of KtrA R16K mutant ring with bound ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s5b
TitleNon-square conformation of KtrA R16K mutant ring with bound ADP
ComponentsKtr system potassium uptake protein A
KeywordsTRANSPORT PROTEIN / RCK domain / potassium homeostasis / cation channel / non-square conformation octameric ring / adp
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
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 ...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'-DIPHOSPHATE / Ktr system potassium uptake protein A
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.052 Å
AuthorsTeixeira-Duarte, C.M. / Fonseca, F. / Morais-Cabral, J.H.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-BQM/29863/2017 Portugal
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-007274 Portugal
CitationJournal: Elife / Year: 2019
Title: Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site.
Authors: Teixeira-Duarte, C.M. / Fonseca, F. / Morais Cabral, J.H.
History
DepositionJul 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,52816
Polymers199,1108
Non-polymers3,4188
Water0
1
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
hetero molecules

C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
hetero molecules

E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,52816
Polymers199,1108
Non-polymers3,4188
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area29450 Å2
ΔGint-246 kcal/mol
Surface area75670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.818, 137.429, 202.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 24888.746 Da / Num. of mol.: 8 / Mutation: R16K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews3/Da)Density % sol (%)
1359.01
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
293.151vapor diffusion100mM HEPES-NaOH pH 7.5, 6% PEG 8000, 20% ethylene glycol
293.152vapor diffusion100mM HEPES-NaOH pH 7.5, 8% PEG 8000, 20% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 3.05→49.51 Å / Num. obs: 46032 / % possible obs: 99.2 % / Redundancy: 8.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.054 / Rrim(I) all: 0.158 / Net I/σ(I): 15.9
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.474 / Num. unique obs: 4076 / CC1/2: 0.886 / Rpim(I) all: 0.249 / Rrim(I) all: 0.538 / % possible all: 91.6

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4j90
Resolution: 3.052→48.168 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0.4 / Phase error: 27.86
RfactorNum. reflection% reflection
Rfree0.2429 4283 5.03 %
Rwork0.2093 --
obs0.211 46032 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.052→48.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13568 0 216 0 13784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314008
X-RAY DIFFRACTIONf_angle_d0.7618960
X-RAY DIFFRACTIONf_dihedral_angle_d13.4795232
X-RAY DIFFRACTIONf_chiral_restr0.0292200
X-RAY DIFFRACTIONf_plane_restr0.0022376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0519-3.08660.53331080.42721722X-RAY DIFFRACTION63
3.0866-3.12290.41521290.42142497X-RAY DIFFRACTION89
3.1229-3.16090.4471580.38062431X-RAY DIFFRACTION89
3.1609-3.20090.39761430.3622542X-RAY DIFFRACTION91
3.2009-3.24310.40841710.35592639X-RAY DIFFRACTION96
3.2431-3.28750.38551450.32422651X-RAY DIFFRACTION95
3.2875-3.33440.37051520.30862661X-RAY DIFFRACTION97
3.3344-3.38420.31911290.28152762X-RAY DIFFRACTION98
3.3842-3.43710.29841540.27352752X-RAY DIFFRACTION98
3.4371-3.49340.27441840.25172662X-RAY DIFFRACTION98
3.4934-3.55360.30441410.24432782X-RAY DIFFRACTION98
3.5536-3.61820.28471270.25652715X-RAY DIFFRACTION99
3.6182-3.68780.31751510.25422758X-RAY DIFFRACTION98
3.6878-3.7630.28261200.26652799X-RAY DIFFRACTION99
3.763-3.84480.27091460.24792745X-RAY DIFFRACTION99
3.8448-3.93420.24721320.22392816X-RAY DIFFRACTION99
3.9342-4.03250.2121330.212765X-RAY DIFFRACTION100
4.0325-4.14150.30161520.1992779X-RAY DIFFRACTION100
4.1415-4.26330.24011630.19072755X-RAY DIFFRACTION100
4.2633-4.40080.23071240.18332804X-RAY DIFFRACTION99
4.4008-4.5580.22761570.16692780X-RAY DIFFRACTION100
4.558-4.74040.23681480.17462771X-RAY DIFFRACTION100
4.7404-4.95590.23131170.17612782X-RAY DIFFRACTION100
4.9559-5.21690.21431860.17742764X-RAY DIFFRACTION100
5.2169-5.54330.20071340.17312796X-RAY DIFFRACTION100
5.5433-5.97060.2141430.19032792X-RAY DIFFRACTION100
5.9706-6.57010.21751310.20042796X-RAY DIFFRACTION100
6.5701-7.51770.19531270.20562786X-RAY DIFFRACTION100
7.5177-9.45970.16631320.15972810X-RAY DIFFRACTION100
9.4597-48.17350.18711460.17992741X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.1403-1.0712-2.78868.0505-1.991310.45420.29770.823-0.2995-0.7452-0.3415-1.14732.06581.71880.01440.93690.4450.0051.22960.01820.7303-11.3031-19.2706-7.2204
24.01253.29953.89681.76561.68767.5148-0.09330.00910.7362-0.0605-0.05230.8212-0.6884-1.1919-0.09940.71710.2040.11180.84990.20230.9076-20.6885-7.37783.7778
38.10783.09041.99613.42190.20383.92240.7687-1.1710.21741.1984-0.54020.425-0.70810.0996-0.1631.0524-0.07170.13710.9709-0.16180.7865-25.1329-17.830131.2552
49.72210.71160.05966.7266-0.36136.55480.24570.45720.96760.0802-0.28351.0392-0.6977-0.43260.05870.54020.0055-0.03480.61390.07220.7401-7.9584.030916.6563
57.54766.13116.87555.82182.03098.70650.06560.2239-0.88560.1576-0.32690.24670.83541.30460.1610.51880.20090.07370.88590.19030.9827-5.8973-14.31112.7124
68.12074.5743-2.77538.34544.20989.2051-0.562-0.1747-0.1661-0.59420.18940.58730.4875-0.050.32010.78830.0876-0.07730.62130.13740.7824-31.839-29.450813.8377
75.3972-0.16880.45545.79012.05488.63470.1722-0.2303-0.06320.9388-0.35080.9211.5531-2.15660.15590.8075-0.3008-0.01691.0506-0.03330.8335-27.2735-9.61577.0741
83.2888-1.1772-2.98591.8804-2.68017.6227-0.1059-0.46040.90780.30670.1026-1.1624-0.79060.9174-0.1020.6179-0.1231-0.06460.8196-0.33471.2839-14.25682.119770.8282
98.0041-1.2307-2.81497.1052-2.87384.66160.27650.86640.6097-0.51010.2882-1.7484-0.32210.6902-0.58240.6389-0.090.02690.9043-0.06551.18831.4535-10.193247.9977
105.0211-1.01924.51057.2878-1.94617.8687-0.57090.29192.98270.2372-0.222-1.4879-1.56930.63160.73590.7539-0.0385-0.02870.66150.04611.6062-19.546313.313553.4829
116.6604-5.33696.10917.1325-3.13686.05840.08430.75550.3276-0.1918-0.4575-0.80120.05050.42550.38910.3966-0.07480.05110.6647-0.02660.7394-22.8654-3.16854.4734
125.9373-2.3808-5.24468.1498-1.04387.5549-0.691-1.93820.17721.10910.8302-1.31630.86241.3711-0.17760.96830.2291-0.37521.0364-0.2170.99650.8012-19.559767.754
139.5442-0.8561-0.72347.46652.9136.69930.25740.71430.4444-0.6846-0.10180.8056-0.907-0.923-0.2190.63860.115-0.06770.62560.17320.6156-32.0562-51.715731.5547
144.40112.3305-3.43711.3819-2.34922.6616-0.0527-0.1437-0.43910.22230.0709-0.82141.21190.9720.06070.80860.1544-0.18640.5474-0.04440.8426-22.248-63.560842.1525
157.48081.996-2.28999.0604-0.17423.66920.8487-1.6555-0.24351.5344-0.5561-0.5781.390.2908-0.38651.2586-0.2185-0.48341.05410.04911.007-17.7194-53.633269.5351
165.82462.00530.565510.77320.29045.10180.1743-0.7156-1.2571.1284-0.3163-1.46910.70460.270.15440.698-0.1162-0.11860.57930.12770.7851-35.0616-75.274854.7843
179.397.2776-4.81945.2705-1.95586.21880.2775-0.71740.8080.4285-0.4614-0.2536-0.33690.15350.27950.54310.067-0.07980.48160.01330.7414-36.9819-56.799251.4351
182.85253.3587-0.48847.4504-2.84166.0198-0.05170.1261-0.279-0.18980.1087-1.08870.01510.8680.01010.5913-0.0471-0.08040.755-0.16590.9436-11.3223-41.908952.3648
199.9191-0.49253.40927.82583.43293.6033-0.475-0.40640.302-0.5546-0.28291.2016-1.8078-1.64910.72610.86170.3373-0.10111.0026-0.03930.7217-71.74213.5318-9.769
204.41664.47130.020910.03815.89349.6783-0.19930.8973-0.5009-0.71330.3251-0.1373-0.63810.2929-0.10230.5480.0897-0.01260.79730.08240.5547-63.10273.7986-17.2631
216.9995-3.2638.78948.1477-8.85992.2049-0.8015-1.6432-1.23080.25350.5368-0.8754-0.27180.95290.16470.66170.2646-0.13571.06430.24281.246-54.8217-2.36034.0327
225.88662.74770.67674.522-4.53158.18470.0171-1.39130.35860.77030.0379-0.5741-0.75950.10240.01020.74050.1467-0.01271.3484-0.01420.8639-41.07447.790916.2002
236.98941.952-5.12228.09281.86516.0563-0.2935-0.7342-1.96270.2709-0.1872-0.73290.83090.68520.3770.60040.1614-0.06461.05180.38391.0814-62.6793-13.7269.3638
249.44468.0582-7.68096.6631-5.38117.9998-0.0881-0.58730.17770.25960.11370.3514-0.447-0.0142-0.07450.54360.1544-0.02180.77710.02050.7115-65.68764.64086.919
258.80980.96123.09536.905-0.68818.7322-0.50921.01690.6352-0.47510.3616-0.3788-0.8730.53470.19390.7408-0.11040.10710.88640.11430.7156-40.388718.2111-2.7168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 222 )
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 106 )
5X-RAY DIFFRACTION5chain 'B' and (resid 107 through 137 )
6X-RAY DIFFRACTION6chain 'B' and (resid 138 through 222 )
7X-RAY DIFFRACTION7chain 'C' and (resid 7 through 106 )
8X-RAY DIFFRACTION8chain 'C' and (resid 107 through 137 )
9X-RAY DIFFRACTION9chain 'C' and (resid 138 through 222 )
10X-RAY DIFFRACTION10chain 'D' and (resid 7 through 94 )
11X-RAY DIFFRACTION11chain 'D' and (resid 95 through 137 )
12X-RAY DIFFRACTION12chain 'D' and (resid 138 through 222 )
13X-RAY DIFFRACTION13chain 'E' and (resid 7 through 106 )
14X-RAY DIFFRACTION14chain 'E' and (resid 107 through 137 )
15X-RAY DIFFRACTION15chain 'E' and (resid 138 through 222 )
16X-RAY DIFFRACTION16chain 'F' and (resid 7 through 106 )
17X-RAY DIFFRACTION17chain 'F' and (resid 107 through 137 )
18X-RAY DIFFRACTION18chain 'F' and (resid 138 through 222 )
19X-RAY DIFFRACTION19chain 'G' and (resid 7 through 66 )
20X-RAY DIFFRACTION20chain 'G' and (resid 67 through 123 )
21X-RAY DIFFRACTION21chain 'G' and (resid 124 through 137 )
22X-RAY DIFFRACTION22chain 'G' and (resid 138 through 222 )
23X-RAY DIFFRACTION23chain 'H' and (resid 7 through 106 )
24X-RAY DIFFRACTION24chain 'H' and (resid 107 through 137 )
25X-RAY DIFFRACTION25chain 'H' and (resid 138 through 222 )

+
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