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- PDB-2zd9: Structure of a Bacterial Cyclic-Nucleotide Regulated Ion Channel -

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Basic information

Entry
Database: PDB / ID: 2zd9
TitleStructure of a Bacterial Cyclic-Nucleotide Regulated Ion Channel
ComponentsMll3241 protein
KeywordsMEMBRANE PROTEIN / Transmembrane protein
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
Voltage-gated potassium channels / Cyclic nucleotide-regulated ion channel, N-terminal / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Helix Hairpins - #70 / Cyclic nucleotide-binding, conserved site / Ion channel / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...Voltage-gated potassium channels / Cyclic nucleotide-regulated ion channel, N-terminal / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Helix Hairpins - #70 / Cyclic nucleotide-binding, conserved site / Ion channel / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Cyclic nucleotide-gated potassium channel mll3241
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4 Å
AuthorsClayton, G.M. / Cabral-Morais, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel.
Authors: Clayton, G.M. / Altieri, S. / Heginbotham, L. / Unger, V.M. / Morais-Cabral, J.H.
History
DepositionNov 21, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Mll3241 protein
B: Mll3241 protein
C: Mll3241 protein
D: Mll3241 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,2619
Polymers151,0654
Non-polymers1955
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)283.287, 283.287, 103.507
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAA11 - 6011 - 60
21TYRTYRLEULEUBB10 - 6010 - 60
31TYRTYRLEULEUCC10 - 6010 - 60
41TYRTYRLEULEUDD10 - 6010 - 60
12LEULEUARGARGAA80 - 11080 - 110
22LEULEUARGARGBB80 - 11080 - 110
32LEULEUARGARGCC80 - 11080 - 110
42LEULEUARGARGDD80 - 11080 - 110
13PHEPHEILEILEAA115 - 200115 - 200
23PHEPHEILEILEBB115 - 200115 - 200
33PHEPHEILEILECC115 - 200115 - 200
43PHEPHEILEILEDD115 - 200115 - 200

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Mll3241 protein


Mass: 37766.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Plasmid: PASK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (RP) / References: UniProt: Q98GN8
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K

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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: 5.29 Å3/Da / Density % sol: 76.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG2000, pH 6.0, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorDetector: CCD / Date: Jan 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 4→141.42 Å / Num. obs: 26095

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 4→141.42 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.883 / SU B: 56.586 / SU ML: 0.748 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.498 / ESU R Free: 0.707 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.333 1324 5.1 %RANDOM
Rwork0.307 ---
obs0.308 26095 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 142.676 Å2
Baniso -1Baniso -2Baniso -3
1--12.14 Å2-6.07 Å20 Å2
2---12.14 Å20 Å2
3---18.21 Å2
Refinement stepCycle: LAST / Resolution: 4→141.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 0 5 0 6701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226840
X-RAY DIFFRACTIONr_angle_refined_deg0.9311.979365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1085909
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72721.481216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95215996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7781552
X-RAY DIFFRACTIONr_chiral_restr0.0530.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025060
X-RAY DIFFRACTIONr_nbd_refined0.1970.23049
X-RAY DIFFRACTIONr_nbtor_refined0.2950.24828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2135
X-RAY DIFFRACTIONr_metal_ion_refined0.2260.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.215
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: MEDIUM POSITIONAL / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A3510.24
12B3510.28
13C3510.26
14D3510.21
21A2430.26
22B2430.25
23C2430.22
24D2430.19
31A6440.26
32B6440.25
33C6440.28
34D6440.26
LS refinement shellResolution: 4→4.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 107 -
Rwork0.45 1844 -
all-1951 -
obs--99.14 %

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