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- PDB-4ys2: RCK domain with CDA -

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Basic information

Entry
Database: PDB / ID: 4ys2
TitleRCK domain with CDA
ComponentsNa+/H+ antiporter-like protein
KeywordsIMMUNE SYSTEM / RCK domain / CDA
Function / homology
Function and homology information


: / antiporter activity / monoatomic cation transmembrane transporter activity / proton transmembrane transport / potassium ion transport / membrane => GO:0016020 / membrane
Similarity search - Function
Regulator of K+ conductance, C-terminal domain / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / 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 ...Regulator of K+ conductance, C-terminal domain / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / 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. / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / Sodium:proton antiporter / Glutathione-regulated potassium-efflux system protein KefC
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.968 Å
AuthorsChin, K.H. / Chou, S.H.
CitationJournal: To Be Published
Title: RCK domain with CDA
Authors: Chin, K.H. / Chou, S.H.
History
DepositionMar 16, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na+/H+ antiporter-like protein
B: Na+/H+ antiporter-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7873
Polymers20,1282
Non-polymers6581
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-6 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.195, 45.843, 69.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Na+/H+ antiporter-like protein / Sodium:proton antiporter


Mass: 10064.084 Da / Num. of mol.: 2 / Fragment: RCK C-terminal domain (UNP RESIDUES 531-614)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pTRH1T / Production host: Escherichia coli (E. coli) / References: UniProt: W8TQN9, UniProt: Q2FZQ4*PLUS
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.64 Å3/Da / Density % sol: 25.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH7.5 and 1.1M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 12747 / % possible obs: 98.9 % / Redundancy: 6.2 % / Net I/σ(I): 24.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.968→18.788 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 946 10 %
Rwork0.2289 --
obs0.2362 9460 96.29 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.767 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5595 Å20 Å2-0 Å2
2--5.6533 Å2-0 Å2
3----0.0938 Å2
Refinement stepCycle: LAST / Resolution: 1.968→18.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 44 23 1281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081238
X-RAY DIFFRACTIONf_angle_d1.1761670
X-RAY DIFFRACTIONf_dihedral_angle_d16.843470
X-RAY DIFFRACTIONf_chiral_restr0.081178
X-RAY DIFFRACTIONf_plane_restr0.005218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9681-2.07170.25661260.21981124X-RAY DIFFRACTION91
2.0717-2.20130.26471250.24051158X-RAY DIFFRACTION93
2.2013-2.3710.28841330.24021184X-RAY DIFFRACTION96
2.371-2.6090.29911330.25871218X-RAY DIFFRACTION97
2.609-2.98530.28591380.26741229X-RAY DIFFRACTION98
2.9853-3.75620.29111400.24031268X-RAY DIFFRACTION99
3.7562-100.28131510.25241333X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -7.9767 Å / Origin y: -0.2102 Å / Origin z: -6.6127 Å
111213212223313233
T0.2213 Å2-0.0186 Å2-0.002 Å2-0.1853 Å2-0.0049 Å2--0.1886 Å2
L2.1389 °2-0.4913 °2-0.737 °2-1.4125 °2-0.0692 °2--1.2486 °2
S-0.0937 Å °0.0208 Å °-0.1091 Å °-0.0145 Å °0.0246 Å °0.0926 Å °0.0997 Å °0.0061 Å °0.0741 Å °
Refinement TLS groupSelection details: all

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