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- PDB-2hmw: Square-shaped octameric ring structure of an RCK domain with ATP bound -

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Basic information

Entry
Database: PDB / ID: 2hmw
TitleSquare-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: 3 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

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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
Water00
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)126.280, 126.280, 98.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsThe biological assembly is an octameric ring generated from the asymmetric unit dimer using these symmetry operators: X, Y, Z and Y, 1-X, Z and 1-X, 1-Y, Z and 1-Y, X, 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

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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: 3.06 Å3/Da / Density % sol: 59.76 %
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

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 8258 / Num. obs: 8231 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Χ2: 1.007 / Net I/σ(I): 11.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.731 / Num. unique all: 799 / Χ2: 1.007 / % possible all: 99.9

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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 from pdb entry 1LSU

1lsu


Resolution: 3→50 Å / FOM work R set: 0.756 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 856 10.3 %RANDOM
Rwork0.264 ---
all0.268 8258 --
obs0.268 8044 97.2 %-
Solvent computationBsol: 50.849 Å2
Displacement parametersBiso mean: 84.146 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 62 0 2190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.312
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3-3.060.532430.359355398
3.06-3.130.348370.374403440
3.13-3.20.374450.383411456
3.2-3.280.409510.356408459
3.28-3.370.347470.345398445
3.37-3.470.353430.31421464
3.47-3.580.351520.25420472
3.58-3.710.225540.278422476
3.71-3.860.4630.293415478
3.86-4.030.353550.279428483
4.03-4.240.285490.264432481
4.24-4.510.294600.256424484
4.51-4.860.261470.217444491
4.86-5.350.26610.227424485
5.35-6.120.347410.267447488
6.12-7.70.271600.251445505
7.7-500.25480.23491539
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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