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- PDB-5f29: Structure of RCK domain with cda -

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Basic information

Entry
Database: PDB / ID: 5f29
TitleStructure of RCK domain with cda
ComponentsNa+/H+ antiporter-like protein
KeywordsTRANSPORT PROTEIN / RCK domain / cda / CpaA
Function / homology
Function and homology information


antiporter activity / monoatomic cation transmembrane transporter activity / proton transmembrane transport / potassium ion transport / 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
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.821 Å
AuthorsChin, K.H.
CitationJournal: Biochemistry / Year: 2015
Title: Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK.
Authors: Chin, K.H. / Liang, J.M. / Yang, J.G. / Shih, M.S. / Tu, Z.L. / Wang, Y.C. / Sun, X.H. / Hu, N.J. / Liang, Z.X. / Dow, J.M. / Ryan, R.P. / Chou, S.H.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site

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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)18,2423
Polymers17,5842
Non-polymers6581
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-7 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.489, 47.297, 70.174
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


Mass: 8791.772 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 400-614
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: kefC, ERS154949_00406
Production host: Escherichia coli O103:H2 str. 12009 (bacteria)
References: UniProt: A0A077VS08, 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.: 57 / 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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tris 0.1M pH 7.0 PEG 4000 15%

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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 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→23.5 Å / Num. obs: 12747 / % possible obs: 98.9 % / Redundancy: 6.3 % / Net I/σ(I): 22

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.821→20.744 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 0 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 1238 9.97 %
Rwork0.2011 --
obs0.2174 12417 96.39 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.628 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6 Å2-0 Å2-0 Å2
2---0.8313 Å2-0 Å2
3----1.7687 Å2
Refinement stepCycle: LAST / Resolution: 1.821→20.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 44 66 1289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081249
X-RAY DIFFRACTIONf_angle_d1.2021693
X-RAY DIFFRACTIONf_dihedral_angle_d17.435470
X-RAY DIFFRACTIONf_chiral_restr0.09182
X-RAY DIFFRACTIONf_plane_restr0.005214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8206-1.89340.30191230.29321085X-RAY DIFFRACTION86
1.8934-1.97950.30181280.26421182X-RAY DIFFRACTION93
1.9795-2.08380.29981320.2551215X-RAY DIFFRACTION96
2.0838-2.21420.26251350.24231238X-RAY DIFFRACTION98
2.2142-2.38490.25591390.22341238X-RAY DIFFRACTION98
2.3849-2.62450.27061410.24791284X-RAY DIFFRACTION99
2.6245-3.00330.28031430.22921282X-RAY DIFFRACTION100
3.0033-3.78010.26771450.19461301X-RAY DIFFRACTION100
3.7801-3.9010.21121520.18631354X-RAY DIFFRACTION98

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