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- PDB-8ayq: NaK C-DI mutant with Rb+ and Ca2+ -

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Basic information

Entry
Database: PDB / ID: 8ayq
TitleNaK C-DI mutant with Rb+ and Ca2+
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / ION CHANNEL / PROKARYOTE / MEMBRANE PROTEIN
Function / homology
Function and homology information


stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / identical protein binding / membrane / metal ion binding
Similarity search - Function
Two pore domain potassium channel / Potassium channel domain / Ion channel
Similarity search - Domain/homology
RUBIDIUM ION / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMinniberger, S. / Plested, A.J.R.
Funding supportEuropean Union, Germany, 4items
OrganizationGrant numberCountry
European Research Council (ERC)647895European Union
German Research Foundation (DFG)291198853 Germany
German Research Foundation (DFG)323514590 Germany
German Research Foundation (DFG)446182550 Germany
CitationJournal: J.Chem.Inf.Model. / Year: 2023
Title: Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel.
Authors: Schackert, F.K. / Biedermann, J. / Abdolvand, S. / Minniberger, S. / Song, C. / Plested, A.J.R. / Carloni, P. / Sun, H.
History
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium channel protein
B: Potassium channel protein
C: Potassium channel protein
D: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,64332
Polymers42,9434
Non-polymers2,70028
Water66737
1
A: Potassium channel protein
B: Potassium channel protein
hetero molecules

A: Potassium channel protein
B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,26740
Polymers42,9434
Non-polymers3,32436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area15140 Å2
ΔGint-411 kcal/mol
Surface area17480 Å2
2
D: Potassium channel protein
hetero molecules

D: Potassium channel protein
hetero molecules

C: Potassium channel protein
hetero molecules

C: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,01924
Polymers42,9434
Non-polymers2,07620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area11420 Å2
ΔGint-260 kcal/mol
Surface area17850 Å2
Unit cell
Length a, b, c (Å)67.570, 175.508, 67.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

RB

21A-202-

RB

31A-203-

CA

41A-204-

CA

51B-201-

CA

61C-201-

RB

71C-202-

RB

81D-201-

CA

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Potassium channel protein


Mass: 10735.706 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_0669 / Plasmid: pQE60 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): NEBExpress Iq / References: UniProt: Q81HW2

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Non-polymers , 5 types, 65 molecules

#2: Chemical
ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.9 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES (NaOH), 40% v/v MPD (2-Methyl-2,4-pentanediol racemate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.815 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2.75→33.78 Å / Num. obs: 18778 / % possible obs: 96.02 % / Redundancy: 2.1 % / Biso Wilson estimate: 70.58 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.1319 / Net I/σ(I): 4.12
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 2 % / Num. unique obs: 984 / CC1/2: 0.397 / CC star: 0.754 / Rpim(I) all: 0.8742 / % possible all: 92.28

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+86 / Resolution: 2.75→33.78 Å / SU ML: 0.6429 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 41.4701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3004 927 4.95 %
Rwork0.2552 17805 -
obs0.2576 18732 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.04 Å2
Refinement stepCycle: LAST / Resolution: 2.75→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 154 37 3083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753084
X-RAY DIFFRACTIONf_angle_d1.16074222
X-RAY DIFFRACTIONf_chiral_restr0.064537
X-RAY DIFFRACTIONf_plane_restr0.0076485
X-RAY DIFFRACTIONf_dihedral_angle_d6.213404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.90.42871310.41612490X-RAY DIFFRACTION91.1
2.9-3.080.45981370.37452633X-RAY DIFFRACTION96.05
3.08-3.310.35151310.33422543X-RAY DIFFRACTION94.39
3.32-3.650.35531310.31542483X-RAY DIFFRACTION91.02
3.65-4.170.32071370.23242616X-RAY DIFFRACTION95.36
4.18-5.260.2571350.19862536X-RAY DIFFRACTION92.81
5.26-33.780.23611250.21832504X-RAY DIFFRACTION91.67
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)
12.92152950984-1.78946216489-1.062157762811.151079150220.3026710909613.736561925760.0754753562362-0.510459595936-0.3016954504360.136947557784-0.329965349659-1.495246095990.000517210195920.0797392191379-0.0003638339027530.6145188711170.02237165248510.003833860211320.690962861495-0.1537756191620.759475667468-4.25353211958-18.63894399911.92806895069
20.834827799935-0.2128847058680.1169388457211.121932250410.7661105448953.723972473760.06768472706870.0224142831958-0.2198062769810.269091681289-0.246021413488-0.208510007303-0.187868446883-0.183588586325-1.65104741073E-50.567774609741-0.0005013810314350.007856698331260.84978897971-0.06996379067150.668214504383-4.98760263443-25.4378164367-6.62517848451
31.978198878530.9893832281380.04711764503220.931625304499-1.077558398392.17894444904-0.5671596708530.3179979634520.334388707649-0.06984298069140.5698078968950.272316666486-0.4339468618930.630839384215-0.0004170936355310.7428654710790.131753702485-0.157802128471.032320631280.02042574878370.809400964723-18.8734586725-19.3532341889-21.2989822064
40.386677519957-0.382792632559-0.01947732404150.2703202589320.01892124888870.118924219209-0.01674624652010.644178489084-0.102941791179-0.2666979293810.9907312969360.1813994695640.0636158307420.9071585952380.001398610714550.6398876039070.00956362244087-0.07251408832580.627078309559-0.02988091101240.694005954382-14.5705385787-32.0029589832-18.7755124393
54.566955880361.892604230750.399054018540.6466964489880.4784196982093.49190901282-0.246743858732-0.08915131911840.3671589472960.1203772742190.1873170835950.2669114718690.5494687748610.231324004655-0.0001894429255280.5610917699030.0473194358776-0.02147979793350.6851451345230.1117931533060.663859074985-8.74823768916-23.0417214675-22.6604273276
65.56937454836-1.71025360191-0.3211267697762.792495934541.31684111282.355037496720.0144271604432-0.431060309231-1.35118328471-0.1235858567220.7048469144110.3672035290851.934627835460.1137109749910.1488620503111.41970005132-0.255215873193-0.4390568421430.0711854722712-0.3755585742111.41143846549-12.0999554768-5.923784114661.16470412397
72.90618138094-1.50375759798-0.9563792692351.8604727111.696493769971.38547200224-0.7016274338051.09981669378-0.1196392196460.8767417343711.6076526416-0.468654613047-0.451155962559-0.5320284092930.0122529226320.773073917046-0.112235262384-0.02083921126331.10079318307-0.09496497141290.638676652793-21.6182316068-24.9286599099-35.7356018369
80.292297551323-0.01675413178210.2557101295150.0238400295163-0.0328630809670.169048589546-0.6444398492571.30572190948-0.196204882267-0.565545527370.516363527198-0.932913471393-0.9632194283680.402045213286-0.000366154425470.961260034557-0.173853002192-0.1125405006480.968953694383-0.2162439821790.807682288146-25.6311976059-11.7456484442-38.8261978953
90.201988286520.225997304508-0.06691256052750.400892836968-0.154035640437-0.002459138437890.7759741413330.1804808892730.4802173938461.81327624501-0.1737278704040.140502224704-1.43612357938-0.4558144560090.002044413310230.884492592302-0.1206862796590.2319574536910.936841365567-0.1885551216450.762896199106-26.7700625899-12.8719840262-46.8045233008
102.6945437767-0.837697373159-0.8796476718240.307245348978-0.770242539170.7183617988030.175531041133-0.193533633538-0.3424032474650.0544411012406-0.07042002811870.0670151172737-0.1192694369450.426677138403-0.0002209313224560.818239597291-0.1649557409160.05802548113770.706867578746-0.1512246224680.638467171147-29.5895218856-28.2014471724-40.6848895947
113.918857635932.60394024521-1.08431166152.496553552830.9350617909582.761831010370.410990066644-0.3155622118330.288079779978-0.00599950746899-0.1862216033560.109310931105-0.5768139881740.789349596526-0.0001461956194270.759874796096-0.2057037177990.06389717424270.758331067754-0.06702025598860.671679359716-19.7998460902-21.50643390026.38255006296
123.777507741460.59579552021-1.086419188651.616416100040.2039073568850.4199117661820.403836426902-1.382552383332.37061315109-0.6209858283220.4495525354490.0197153095667-0.3218266017440.2149063056510.9275461631141.08071094278-0.4335556696660.06002796373570.3534478768490.2547480010111.06683072443-30.1695738907-12.86862485829.77206240823
133.710727665021.0779662193-0.6421669820731.407071494391.758728938293.099988989610.4750051087180.1220603319980.219063303297-0.197757062191-0.4456938198190.324896863994-0.09639839025150.111423359488-0.0001672021589730.706677990535-0.1144443857120.09566883489760.659703212788-0.02144376806510.533753885131-28.3309027003-23.77191228026.46667301386
14-0.0788130640041-0.1047325820720.04446775848030.167263025635-0.05724857413230.1415567882980.9768520387431.66386974546-0.3401314694181.57820486982-0.01208771089890.725127146920.646558845192-0.5582052639750.009901586096660.9157970546370.162101724771-0.02011086751761.209553774830.02982573671440.611221956455-14.5289019648-37.482419084626.1691929042
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 20 through 45 )AA20 - 451 - 26
22chain 'A' and (resid 46 through 99 )AA46 - 9927 - 80
33chain 'B' and (resid 21 through 45 )BB21 - 451 - 25
44chain 'B' and (resid 46 through 59 )BB46 - 5926 - 39
55chain 'B' and (resid 60 through 99 )BB60 - 9940 - 79
66chain 'B' and (resid 100 through 112 )BB100 - 11280 - 92
77chain 'C' and (resid 20 through 45 )CC20 - 451 - 26
88chain 'C' and (resid 46 through 60 )CC46 - 6027 - 41
99chain 'C' and (resid 61 through 72 )CC61 - 7242 - 53
1010chain 'C' and (resid 73 through 112 )CC73 - 11254 - 93
1111chain 'D' and (resid 19 through 60 )DD19 - 601 - 42
1212chain 'D' and (resid 61 through 72 )DD61 - 7243 - 54
1313chain 'D' and (resid 73 through 99 )DD73 - 9955 - 81
1414chain 'D' and (resid 100 through 112 )DD100 - 11282 - 94

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