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- PDB-1u12: M. loti cyclic nucleotide binding domain mutant -

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Basic information

Entry
Database: PDB / ID: 1u12
TitleM. loti cyclic nucleotide binding domain mutant
Componentscyclic nucleotide binding domain
KeywordsMEMBRANE PROTEIN / mutant cyclic nucleotide binding domain / C-helix mutation / unliganded
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 / Jelly Rolls ...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
IODIDE ION / : / Cyclic nucleotide-gated potassium channel mll3241
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 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
DepositionJul 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cyclic nucleotide binding domain
B: cyclic nucleotide binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,27439
Polymers28,9912
Non-polymers4,28337
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.126, 57.126, 193.037
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-920-

K

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Components

#1: Protein cyclic nucleotide binding domain


Mass: 14495.732 Da / Num. of mol.: 2
Fragment: cyclic nucleotide binding domain, cytoplasmic domain
Mutation: R348A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RP / References: UniProt: Q98GN8
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: HEPES buffer, NaCl, Potassium Thiocyanate, Ammonium Sulphate, Ethylene Glycol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.964, 0.979, 0.9788
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9641
20.9791
30.97881
ReflectionResolution: 2.6→40.39 Å / Num. all: 18610 / Num. obs: 16180 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 23.6 Å2 / Limit h max: 21 / Limit h min: 1 / Limit k max: 15 / Limit k min: 1 / Limit l max: 73 / Limit l min: -74 / Observed criterion F max: 1229528.12 / Observed criterion F min: 5.1
Reflection shellResolution: 2.6→2.87 Å / Redundancy: 6 % / Mean I/σ(I) obs: 6 / Rsym value: 0.488 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→40.39 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 0.01 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Friedel's pairs were used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2814 810 5 %RANDOM
Rwork0.2533 ---
all0.2814 16767 --
obs0.2533 16180 96.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 27.4384 Å2 / ksol: 0.371517 e/Å3
Displacement parametersBiso max: 82.9 Å2 / Biso mean: 32.9 Å2 / Biso min: 1.54 Å2
Baniso -1Baniso -2Baniso -3
1-6.07 Å20 Å20 Å2
2--6.07 Å20 Å2
3----12.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.35 Å
Luzzati d res high-2.7
Refinement stepCycle: LAST / Resolution: 2.7→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 45 11 1918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_torsion_deg24.7
X-RAY DIFFRACTIONx_torsion_impr_deg2.11
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 (%)
2.7-2.820.4121125.60.31718720.0392111198494
2.82-2.970.3011125.60.28818840.0282102199695
2.97-3.160.37723.60.29919240.0442087199695.6
3.16-3.40.3510350.30819390.0352099204297.3
3.4-3.740.296994.80.2719460.032088204597.9
3.74-4.280.232934.50.22819580.0242100205197.7
4.28-5.40.2381055.20.23119280.0232093203397.1
5.4-40.390.2491145.60.2519190.0232098203396.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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