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- PDB-4j91: Diamond-shaped octameric structure of KtrA with ADP bound -

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Basic information

Entry
Database: PDB / ID: 4j91
TitleDiamond-shaped octameric structure of KtrA with ADP bound
ComponentsKtr system potassium uptake protein A
KeywordsMETAL TRANSPORT / Diamond-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'-DIPHOSPHATE / Ktr system potassium uptake protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.93 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 1.2Nov 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 / 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
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3768
Polymers99,6674
Non-polymers1,7094
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,75216
Polymers199,3348
Non-polymers3,4188
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)147.932, 84.630, 113.675
Angle α, β, γ (deg.)90.000, 128.370, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
/ NCS ensembles :
ID
1
2

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Components

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


Mass: 24916.760 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 (DE3) / References: UniProt: O32080
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.8 Å3/Da / Density % sol: 56.05 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M citrate pH5.6, 14.5% polyethylene glycol 2000, 0.2M ammonium sulphate, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.781→89.123 Å / Num. all: 27727 / Num. obs: 27727 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0.9 / Redundancy: 4.9 % / Rsym value: 0.053 / Net I/σ(I): 21.6
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
2.78-2.934.80.9250.8270.91930740040.410.9250.8272.399.1
2.93-3.114.90.4770.4271.81889738190.210.4770.4274.299.9
3.11-3.324.90.2540.2273.41758235750.1130.2540.2277.699.9
3.32-3.594.90.120.1077.11633133460.0540.120.1071599.8
3.59-3.934.90.0780.0710.71520530960.0350.0780.0720.999.7
3.93-4.44.90.0420.03718.81356127790.0190.0420.03732.899.9
4.4-5.084.90.0320.02923.91198124590.0140.0320.0294299.9
5.08-6.224.90.0290.02625.51030421210.0130.0290.02642.499.9
6.22-8.84.80.0230.02127.5774716260.0110.0230.02151.399.9
8.8-42.3154.50.0210.01831.340449020.010.0210.01871.497.6

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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: 2HMT, 2HMU, 2HMV

2hmt

2hmu

2hmv


Resolution: 2.93→89.12 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.2616 / WRfactor Rwork: 0.2358 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.782 / SU B: 44.29 / SU ML: 0.384 / SU R Cruickshank DPI: 0.4183 / SU Rfree: 0.4501 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 1193 5 %RANDOM
Rwork0.2516 ---
all0.253 23792 --
obs0.253 23792 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 245.02 Å2 / Biso mean: 96.577 Å2 / Biso min: 22.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å20 Å20.5 Å2
2---1.34 Å20 Å2
3---4.8 Å2
Refinement stepCycle: LAST / Resolution: 2.93→89.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6626 0 108 0 6734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196735
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9789123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27125.254295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.811151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2481528
X-RAY DIFFRACTIONr_chiral_restr0.0990.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024906
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A10385.81
12B103810.03
13C10389.09
14D10388.3
21A39613.31
22B39616.7
23C39616.2
24D3967.51
LS refinement shellResolution: 2.93→3.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 79 -
Rwork0.356 1607 -
all-1686 -
obs--99.88 %
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)
15.53810.512-0.40344.4892.52523.8412-0.37870.03980.4018-0.05190.07520.5479-0.8107-0.18110.30350.33640.0714-0.1010.03160.00430.320921.365343.5005-14.8893
212.2878-3.2004-2.254921.8591-8.62734.5019-1.06990.7191-0.07610.36831.26140.58660.0371-0.9525-0.19150.36610.2053-0.23260.6756-0.23570.563913.454533.4765-21.6918
31.0921-1.11331.37153.6406-2.1274.3093-0.12990.3111-0.1704-0.43890.063-0.07310.0560.19310.06690.1479-0.12370.04840.1695-0.08130.251728.219525.376-17.6741
421.1065-5.73821.139221.526716.407145.7972.212-0.4607-2.0096-4.8187-0.4390.4951-2.5556-1.1135-1.77311.16510.0234-0.03640.36760.22371.288748.366726.2895-17.4284
517.1028-3.2589-9.57111.407-10.990825.443-2.1977-0.8229-0.61481.5918-0.469-1.15921.5172.70532.66670.98770.48470.08790.54780.30010.823165.016425.751-10.9057
68.07562.0139-1.135314.0976-9.64678.6104-0.6194-0.8997-0.53350.43530.1139-0.9002-0.10560.48660.50550.13480.16270.14960.49230.24010.803359.645228.0178-12.4412
73.7436-1.4807-0.63242.9276-0.69774.13140.2250.1545-0.4759-0.36990.08920.15920.54610.1127-0.31420.14320.0066-0.06950.0395-0.08420.259430.80999.6985-3.7703
812.3891-2.6124-2.64589.6628-3.63298.5754-0.2407-0.5152-0.41910.04620.05360.0568-0.00370.49180.18710.09490.0496-0.07740.076-0.05780.217936.152912.53683.5111
96.2720.792.13841.6409-1.04896.3820.0801-0.3613-0.27090.24950.306-0.05260.2307-0.1777-0.38610.12950.0559-0.01990.1197-0.02850.231131.883219.10777.4439
100.8718-0.43332.06140.5352-0.96136.3119-0.27210.0785-0.06820.26190.1373-0.1896-0.72460.32310.13480.2517-0.0237-0.05670.1441-0.09160.268832.208131.1028-2.6245
118.80310.346-2.15063.94830.41848.2855-0.36010.5279-1.1846-0.22890.11060.2768-0.1623-0.49890.24960.2061-0.15350.15240.1627-0.15520.355447.456836.2482-28.6581
123.6449-3.1822.18928.331-0.32037.28120.10770.4374-0.57220.3644-0.17140.3760.58690.11540.06370.2314-0.17590.12080.2895-0.22430.373949.561734.1359-31.5394
132.737-0.2733-0.03736.51851.04993.879-0.155-0.0294-0.3832-0.168-0.1869-0.24640.2190.08230.34190.16560.16860.07230.20180.09080.23877.83398.768526.7531
144.0727-1.31890.73944.11130.59764.8753-0.294-0.1571-0.8239-0.29590.06220.66980.0493-0.45720.23180.10660.05760.02790.23290.05850.2745-4.224110.201526.0221
155.12551.6137-1.38474.56930.20420.53970.0043-0.4210.24220.08730.01080.3055-0.0916-0.0072-0.01510.1660.2162-0.06650.3886-0.02260.1783-1.753725.090530.6278
160.5151-0.13462.23277.7635-2.507210.21250.1014-0.0483-0.03450.4875-0.1841-0.60950.0365-0.15980.08260.47330.0599-0.18080.53430.0320.097119.904430.038544.0828
170.17010.3871-0.94055.55512.612910.25120.08880.00020.0095-1.1785-0.287-0.1062-1.2677-0.16210.19820.7034-0.0731-0.2150.55670.19130.498931.349430.029159.1873
180.91812.2798-0.19167.70450.13252.47340.2527-0.3087-0.2713-0.3727-0.5041-1.4661-0.29290.26140.25130.7052-0.1799-0.0560.67780.17440.751930.399926.725553.8226
192.8066-0.4607-0.18113.2702-0.32944.668-0.1223-0.10980.41940.1940.1082-0.0624-0.61350.04330.01410.24360.0917-0.0310.0707-0.04740.125619.127740.522824.4913
203.41361.3779-2.45461.7376-0.52891.9789-0.0075-0.3677-0.34750.0151-0.0433-0.5295-0.0740.22590.05090.17820.1509-0.01760.30230.07380.233818.719622.750528.7714
2134.0784-6.2892-9.26752.9937-1.37479.5643-1.2487-0.1787-1.34261.25330.5673-0.2637-0.90970.39980.68140.71390.4628-0.38240.9066-0.28120.659317.816616.333649.5136
224.4812.7059-5.07665.9984-12.562526.5171-1.501-0.01710.53550.0249-0.5424-0.6607-0.2341.53152.04341.16110.06960.04641.28660.2251.3299-1.174118.041658.9803
232.5354.02623.082514.0104-3.291914.63770.2239-0.8947-0.53961.3790.4367-0.4228-0.81-1.739-0.66060.89450.25550.03031.53230.50710.260910.081118.180162.2555
2410.09436.02514.63175.18312.71722.94650.4553-1.3577-0.59580.9488-0.42570.00510.0242-0.3256-0.02970.73870.1068-0.02270.78710.28050.22288.315618.09456.59
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 77
2X-RAY DIFFRACTION2A78 - 96
3X-RAY DIFFRACTION3A97 - 142
4X-RAY DIFFRACTION4A143 - 155
5X-RAY DIFFRACTION5A156 - 174
6X-RAY DIFFRACTION6A177 - 222
7X-RAY DIFFRACTION7B8 - 65
8X-RAY DIFFRACTION8B66 - 79
9X-RAY DIFFRACTION9B80 - 104
10X-RAY DIFFRACTION10B105 - 138
11X-RAY DIFFRACTION11B139 - 173
12X-RAY DIFFRACTION12B174 - 222
13X-RAY DIFFRACTION13C8 - 45
14X-RAY DIFFRACTION14C46 - 99
15X-RAY DIFFRACTION15C100 - 127
16X-RAY DIFFRACTION16C128 - 157
17X-RAY DIFFRACTION17C161 - 182
18X-RAY DIFFRACTION18C183 - 222
19X-RAY DIFFRACTION19D8 - 96
20X-RAY DIFFRACTION20D97 - 143
21X-RAY DIFFRACTION21D144 - 157
22X-RAY DIFFRACTION22D158 - 166
23X-RAY DIFFRACTION23D167 - 185
24X-RAY DIFFRACTION24D186 - 222

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