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- PDB-4j90: Square-shaped octameric structure of KtrA with ATP bound -

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Basic information

Entry
Database: PDB / ID: 4j90
TitleSquare-shaped octameric structure of KtrA with ATP bound
ComponentsKtr system potassium uptake protein A
KeywordsMETAL TRANSPORT / Square-shaped octameric ring / RCK domain / potassium transport regulation / KtrB membrane protein / cytosol
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'-TRIPHOSPHATE / Ktr system potassium uptake protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.24 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 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8484
Polymers49,8342
Non-polymers1,0142
Water543
1
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,39216
Polymers199,3348
Non-polymers4,0578
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 area31140 Å2
ΔGint-209 kcal/mol
Surface area76160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.838, 122.838, 84.123
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain: (Details: A)

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Components

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


Mass: 24916.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O32080
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 3.18 Å3/Da / Density % sol: 61.37 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH7.5, 3% polyethylene glycol 6000, 2.5% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.097→86.86 Å / Num. all: 11441 / Num. obs: 11441 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0.9 / Redundancy: 3.5 % / Rsym value: 0.052 / Net I/σ(I): 16.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.1-3.263.60.9910.8390.9584916450.5230.9910.8391.699.3
3.26-3.463.60.4080.3452.2561115780.2150.4080.3453.899.8
3.46-3.73.60.2340.1983.8525714770.1240.2340.1986.799.8
3.7-43.50.1370.1166.7490613820.0720.1370.11610.999.6
4-4.383.50.0740.06311.9457212880.0390.0740.0631899.9
4.38-4.93.50.0470.03918.3400311330.0240.0470.03925.899.7
4.9-5.653.50.0430.03719.2364110320.0230.0430.03727.899.9
5.65-6.933.50.0370.03121.729858570.0190.0370.03131.599.5
6.93-9.793.50.0250.02226.423226710.0130.0250.02246.599.4
9.79-45.9963.30.0220.0183312423780.0120.0220.01855.197.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.24→86.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2285 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8165 / SU B: 52.497 / SU ML: 0.407 / SU R Cruickshank DPI: 0.3937 / SU Rfree: 0.475 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 477 4.8 %RANDOM
Rwork0.1903 ---
all0.1927 10041 --
obs0.1927 10041 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.19 Å2 / Biso mean: 109.867 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 3.24→86.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 62 3 3477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193499
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.9844748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0425432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81925.455154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88215627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2851513
X-RAY DIFFRACTIONr_chiral_restr0.0730.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022547
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1675 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.20.5
MEDIUM THERMAL5.922
LS refinement shellResolution: 3.24→3.324 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 33 -
Rwork0.325 702 -
all-735 -
obs--99.86 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.95871.43442.17691.8994-0.98654.23930.08030.84740.227-0.5725-0.23230.15670.08550.20490.1520.36560.1966-0.00470.2326-0.03820.08319.4781-17.782-23.7449
27.61752.0735-0.77564.91855.91258.7485-0.35770.2250.12210.2036-0.49490.72520.5321-0.72750.85260.24630.0885-0.08150.1591-0.15410.246510.1481-25.0924-14.536
33.91961.17861.25823.2304-0.87791.00120.2114-0.0508-0.0068-0.3039-0.06310.23330.1522-0.0175-0.14820.17770.02310.05190.1082-0.06050.123222.3038-24.0201-6.9517
47.26721.8446-0.58375.54140.07694.4484-0.4967-0.0980.6270.48270.262-0.46830.60720.38710.23470.20870.142-0.03160.13560.05710.218447.3835-18.62480.5305
566.9194-5.8034-0.4737.02376.40396.2171-0.8351-1.3827-0.9141-0.16730.57750.42-0.17610.58530.25760.52910.32380.03120.44220.10420.328461.6045-23.76652.351
61.70410.92070.81062.64512.50872.3967-0.1430.07570.16750.18740.4921-0.41070.22180.5351-0.34910.1270.19290.06580.34930.14190.370754.621-19.2516-0.9268
71.533-1.30470.17594.628-1.4392.84690.0045-0.26180.23510.777-0.2021-0.094-0.008-0.53220.19750.2096-0.16750.04330.3099-0.15730.119724.2378-7.53739.3837
83.79520.70542.897810.0254-1.37132.5853-0.0079-0.26420.70920.5565-0.637-0.7746-0.0399-0.08660.6450.2038-0.06980.02570.3891-0.29260.469531.0656-1.36077.8052
93.70491.77992.28954.5517-0.80135.3149-0.06340.10810.4571-0.1703-0.3644-0.563-0.0765-0.0010.42780.0545-0.01430.09620.14020.03460.366930.50790.7253-4.2291
105.9684-4.58531.79398.4463-1.30341.40790.16830.573-0.2205-0.6341-0.2273-0.02320.39040.21780.0590.41710.16630.16470.20930.02470.092239.2034-27.049-15.3706
1117.8141-9.97064.972256.8166-3.50651.4091.3814-0.3558-0.0533-0.8367-1.3570.07850.43780.005-0.02440.36880.31930.12430.67630.04010.169753.7496-38.7557-16.5708
122.99191.2801-0.17845.39231.22923.4153-0.14610.3945-0.27310.0317-0.1506-0.570.6724-0.04150.29670.45480.24120.190.2780.08420.153546.3331-34.8612-13.7656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 80
2X-RAY DIFFRACTION2A81 - 94
3X-RAY DIFFRACTION3A95 - 137
4X-RAY DIFFRACTION4A138 - 166
5X-RAY DIFFRACTION5A167 - 173
6X-RAY DIFFRACTION6A174 - 222
7X-RAY DIFFRACTION7B6 - 66
8X-RAY DIFFRACTION8B67 - 79
9X-RAY DIFFRACTION9B80 - 126
10X-RAY DIFFRACTION10B127 - 165
11X-RAY DIFFRACTION11B166 - 173
12X-RAY DIFFRACTION12B174 - 222

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