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- PDB-2hmv: Diamond-shaped octameric ring structure of an RCK domain with ADP... -

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Basic information

Entry
Database: PDB / ID: 2hmv
TitleDiamond-shaped octameric ring structure of an RCK domain with ADP bound
ComponentsYuaA proteinYuya
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
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 / NAD(P)-binding domain superfamily / Rossmann fold ...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 / NAD(P)-binding domain superfamily / Rossmann fold / 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 / Resolution: 2.2 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)33,0074
Polymers32,1532
Non-polymers8542
Water2,414134
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)132,02916
Polymers128,6128
Non-polymers3,4188
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)127.464, 127.464, 51.401
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 / Yuya


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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.25 Å3/Da / Density % sol: 62.11 %
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: 2.2→50 Å / Num. all: 22465 / Num. obs: 21918 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.094 / Χ2: 0.987 / Net I/σ(I): 12.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.811 / Num. unique all: 2169 / Χ2: 1.079 / % possible all: 99

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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: 2.2→50 Å / FOM work R set: 0.853 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2002 9 %RANDOM
Rwork0.228 ---
all0.229 22465 --
obs0.229 20328 91.8 %-
Solvent computationBsol: 40.424 Å2
Displacement parametersBiso mean: 51.572 Å2
Baniso -1Baniso -2Baniso -3
1-2.881 Å20 Å20 Å2
2--2.881 Å20 Å2
3----5.763 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 54 134 2332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 40

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.2-2.220.374480.295413461
2.22-2.240.295350.298402437
2.24-2.260.19430.27429472
2.26-2.280.29440.275425469
2.28-2.30.268450.254406451
2.3-2.320.234460.271427473
2.32-2.350.229460.263435481
2.35-2.370.379490.27413462
2.37-2.40.256460.229413459
2.4-2.420.271530.279413466
2.42-2.450.329510.265438489
2.45-2.480.244440.257441485
2.48-2.510.293560.284443499
2.51-2.540.258520.269428480
2.54-2.570.257440.259451495
2.57-2.610.339440.265445489
2.61-2.650.325420.23463505
2.65-2.690.224330.247490523
2.69-2.730.283450.274461506
2.73-2.770.242560.265464520
2.77-2.820.335550.29475530
2.82-2.870.32470.296454501
2.87-2.930.244600.276482542
2.93-2.990.324390.31475514
2.99-3.050.269540.253460514
3.05-3.120.32490.253492541
3.12-3.20.307610.256458519
3.2-3.290.273470.249492539
3.29-3.380.235680.241463531
3.38-3.490.211550.219470525
3.49-3.620.23520.221509561
3.62-3.760.218640.21462526
3.76-3.930.234530.2484537
3.93-4.140.198500.201494544
4.14-4.40.185480.165491539
4.4-4.740.174510.154491542
4.74-5.210.229640.169482546
5.21-5.970.227600.232499559
5.97-7.520.254480.227515563
7.52-500.262550.233478533
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3adp_ADJUSTED.param

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