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- PDB-1vp6: M.loti ion channel cylic nucleotide binding domain -

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Basic information

Entry
Database: PDB / ID: 1vp6
TitleM.loti ion channel cylic nucleotide binding domain
ComponentsCyclic-nucleotide binding domain of mesorhizobium loti CNG potassium channel
KeywordsMEMBRANE PROTEIN / Dimer Helical bundle beta barrel core with cyclic AMP bound
Function / homology
Function and homology information


intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / potassium channel activity / cGMP binding / cAMP binding / protein-containing complex binding / identical protein binding / plasma membrane
Similarity search - Function
Cyclic nucleotide-regulated ion channel, N-terminal / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...Cyclic nucleotide-regulated ion channel, N-terminal / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Cyclic nucleotide-gated potassium channel mll3241
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsClayton, G.M. / Silverman, W.R. / Heginbotham, L. / Morais-Cabral, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structural basis of ligand activation in a cyclic nucleotide regulated potassium channel.
Authors: Clayton, G.M. / Silverman, W.R. / Heginbotham, L. / Morais-Cabral, J.H.
History
DepositionOct 14, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionOct 26, 2004ID: 1PF0
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic-nucleotide binding domain of mesorhizobium loti CNG potassium channel
C: Cyclic-nucleotide binding domain of mesorhizobium loti CNG potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,10120
Polymers29,1642
Non-polymers1,93718
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.324, 80.292, 50.419
Angle α, β, γ (deg.)90.00, 99.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyclic-nucleotide binding domain of mesorhizobium loti CNG potassium channel / CNBD


Mass: 14581.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RP / References: UniProt: Q98GN8
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Na acetate, LiCl, ammonium sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.90590, 0.964, 0.9788, 0.9791
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2002
RadiationMonochromator: Si(111) crystals / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.90591
20.9641
30.97881
40.97911
ReflectionResolution: 1.7→33.89 Å / Num. all: 58881 / Num. obs: 58881 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.6 Å2 / Limit h max: 20 / Limit h min: 0 / Limit k max: 47 / Limit k min: 0 / Limit l max: 29 / Limit l min: -29 / Observed criterion F max: 659095.56 / Observed criterion F min: 5.4 / Rsym value: 0.058 / Net I/σ(I): 7.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.177 / % possible all: 94.1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→33.89 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2211 4.9 %random
Rwork0.19 ---
obs0.219 45010 92.5 %-
all-58469 --
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 39.2681 Å2 / ksol: 0.348445 e/Å3
Displacement parametersBiso max: 88.55 Å2 / Biso mean: 19.46 Å2 / Biso min: 1.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å2-1.46 Å2
2--4.17 Å20 Å2
3----2.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Luzzati d res high-1.7
Refinement stepCycle: LAST / Resolution: 1.7→33.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 60 262 2316
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg21.7
X-RAY DIFFRACTIONx_torsion_impr_deg1.18
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.7-1.780.3012674.80.25253260.0187281559376.8
1.78-1.870.2882895.10.23353660.0177391565576.5
1.87-1.990.2372925.20.19353100.0147261560277.1
1.99-2.140.22128250.18253950.0137352567777.2
2.14-2.360.2622624.70.253380.0167278560076.9
2.36-2.70.2242614.60.19754020.0147343566377.1
2.7-3.40.23928350.20953760.0147340565977.1
3.4-33.890.1992754.90.18752840.0127285555976.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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