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- PDB-3cl1: M. loti cyclic-nucleotide binding domain, cyclic-GMP bound -

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Basic information

Entry
Database: PDB / ID: 3cl1
TitleM. loti cyclic-nucleotide binding domain, cyclic-GMP bound
ComponentsMll3241 protein
KeywordsMEMBRANE PROTEIN / cyclic-nucleotide binding
Function / homology
Function and homology information


potassium channel activity / cAMP 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
: / CYCLIC GUANOSINE MONOPHOSPHATE / N-PROPANOL / Cyclic nucleotide-gated potassium channel mll3241
Similarity search - Component
Biological speciesRhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsClayton, G.M. / Alteiri, S.L. / Thomas, L.R. / Morais-Cabral, J.H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural and Energetic Analysis of Activation by a Cyclic Nucleotide Binding Domain.
Authors: Altieri, S.L. / Clayton, G.M. / Silverman, W.R. / Olivares, A.O. / De La Cruz, E.M. / Thomas, L.R. / Morais-Cabral, J.H.
History
DepositionMar 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.3Feb 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,61710
Polymers29,6782
Non-polymers9398
Water1,964109
1
A: Mll3241 protein
hetero molecules

B: Mll3241 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,61710
Polymers29,6782
Non-polymers9398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area3572 Å2
ΔGint-34.9 kcal/mol
Surface area12134 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.202, 79.594, 49.984
Angle α, β, γ (deg.)90.00, 99.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGALAALA4AA225 - 25310 - 38
21ARGARGALAALA4BB225 - 25310 - 38
32VALVALLEULEU1AA256 - 32241 - 107
42VALVALLEULEU1BB256 - 32241 - 107
53HISHISARGARG4AA323 - 349108 - 134
63HISHISARGARG4BB323 - 349108 - 134

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mll3241 protein


Mass: 14839.093 Da / Num. of mol.: 2
Fragment: cyclic nucleotide binding domain, UNP residues 216-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium loti (bacteria) / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q98GN8

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Non-polymers , 5 types, 117 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE / Cyclic guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O7P
#5: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL / Propan-1-ol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIDEL PAIRS
Crystal growDetails: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9
DetectorDate: Apr 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→49.326 Å / Num. obs: 15482 / % possible obs: 87 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 2
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 3 / Rsym value: 0.155 / % possible all: 64.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALAdata scaling
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30.98 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.853 / SU B: 7.595 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.776 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.256 439 4.5 %RANDOM
Rwork0.209 ---
obs0.211 15242 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.58 Å2
2--0.79 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 55 109 2055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3092.0092747
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4385260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6921.47168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91715292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4571519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021499
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.2988
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21395
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0780.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4641.51308
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92922097
X-RAY DIFFRACTIONr_scbond_it1.6683705
X-RAY DIFFRACTIONr_scangle_it3.0074.5650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
463tight positional0.050.05
402medium positional0.290.5
463tight thermal0.080.5
402medium thermal0.552
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 34 -
Rwork0.228 640 -
obs--88.92 %

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