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- PDB-2hmu: Diamond-shaped octameric ring structure of an RCK domain with ATP... -

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Basic information

Entry
Database: PDB / ID: 2hmu
TitleDiamond-shaped octameric ring structure of an RCK domain with ATP bound
ComponentsYuaA protein
KeywordsTRANSPORT PROTEIN / RCK / KTN / KTR / KTRA / KTRAB / membrane protein / ion transporter / symporter
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
: / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...: / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 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 / Resolution: 2.25 Å
AuthorsAlbright, R.A. / Morais-Cabral, J.H.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2006
Title: The RCK Domain of the KtrAB K(+) Transporter: Multiple Conformations of an Octameric Ring.
Authors: Albright, R.A. / Ibar, J.L. / Kim, C.U. / Gruner, S.M. / Morais-Cabral, J.H.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2002
Title: A Mechanism of Regulating Transmembrane Potassium Flux through a Ligand-Mediated Conformational Switch
Authors: Roosild, T.P. / Miller, S. / Booth, I.R. / Choe, S.
#2: Journal: Nature / Year: 2002
Title: Crystal structure and mechanism of a calcium-gated potassium channel
Authors: Jiang, Y. / Lee, A. / Chen, J. / Cadene, M. / Chait, B.T. / MacKinnon, R.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: 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: YuaA protein
B: YuaA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1674
Polymers32,1532
Non-polymers1,0142
Water2,126118
1
A: YuaA protein
B: YuaA protein
hetero molecules

A: YuaA protein
B: YuaA protein
hetero molecules

A: YuaA protein
B: YuaA protein
hetero molecules

A: YuaA protein
B: YuaA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,66916
Polymers128,6128
Non-polymers4,0578
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation5_756-x+2,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)127.668, 127.668, 51.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
DetailsThe biological assembly is an octameric ring generated from the asymmetric unit dimer using these symmetry operators: X, Y, Z and 2-X, Y, 1-Z and 2-X, 1-Y, Z and X, 1-Y, 1-Z

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Components

#1: Protein YuaA protein


Mass: 16076.447 Da / Num. of mol.: 2 / Fragment: RCK CORE DOMAIN (KTN), residues 1-144 / Mutation: C22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yuaA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32080
#2: Chemical ChemComp-ATP / ADENOSINE-5'-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


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 500mM MgCl2, 50mM Tris pH 8.8, 8.5% (w/v) PEG 2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 21175 / Num. obs: 20614 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.099 / Χ2: 1.005 / Net I/σ(I): 11.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.637 / Num. unique all: 1992 / Χ2: 1 / % possible all: 96.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: single domain of PDB entry 1LSU

1lsu


Resolution: 2.25→50 Å / FOM work R set: 0.861 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1893 9 %RANDOM
Rwork0.228 ---
all-21175 --
obs-19221 91.7 %-
Solvent computationBsol: 46.143 Å2
Displacement parametersBiso mean: 51.694 Å2
Baniso -1Baniso -2Baniso -3
1-3.621 Å20 Å20 Å2
2--3.621 Å20 Å2
3----7.241 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 62 118 2324
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 37

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.25-2.270.339400.334410450
2.27-2.290.287380.301430468
2.29-2.310.222400.248410450
2.31-2.340.301430.262439482
2.34-2.360.328450.3396441
2.36-2.390.262470.292417464
2.39-2.410.265470.321414461
2.41-2.440.371580.319409467
2.44-2.470.292460.287447493
2.47-2.50.267450.288426471
2.5-2.530.368370.282452489
2.53-2.560.364470.305432479
2.56-2.60.238520.255451503
2.6-2.640.247440.253446490
2.64-2.680.289370.286460497
2.68-2.720.277520.272468520
2.72-2.760.286380.297471509
2.76-2.810.311530.283468521
2.81-2.860.289480.285455503
2.86-2.920.226550.246465520
2.92-2.980.265590.28465524
2.98-3.040.292610.238471532
3.04-3.110.307610.265474535
3.11-3.190.259480.241492540
3.19-3.270.242590.254492551
3.27-3.370.298570.263495552
3.37-3.480.226510.232507558
3.48-3.60.262610.23499560
3.6-3.750.194550.205506561
3.75-3.920.235630.204496559
3.92-4.130.244480.193513561
4.13-4.380.193470.175524571
4.38-4.720.173610.152519580
4.72-5.20.181700.179503573
5.2-5.950.23550.212531586
5.95-7.490.285620.224539601
7.49-500.242630.217536599
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3atp_ADJUSTED.param

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