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- PDB-2dpq: The crystal structures of the calcium-bound con-G and con-T(K7gam... -

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Basic information

Entry
Database: PDB / ID: 2dpq
TitleThe crystal structures of the calcium-bound con-G and con-T(K7gamma) dimeric peptides demonstrate a novel metal-dependent helix-forming motif
ComponentsConantokin-G
KeywordsMETAL BINDING PROTEIN / conantoxin / con-G / NMDAR antagonist / Gla-containing
Function / homologyConantokin, conserved site / Conantokin family signature. / host cell postsynaptic membrane / ion channel regulator activity / toxin activity / extracellular region / metal ion binding / Conantokin-G
Function and homology information
Biological speciesConus geographus (geography cone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsCnudde, S.E. / Prorok, M. / Dai, Q. / Castellino, F.J. / Geiger, J.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: The crystal structures of the calcium-bound con-G and con-T[K7gamma] dimeric peptides demonstrate a metal-dependent helix-forming motif
Authors: Cnudde, S.E. / Prorok, M. / Dai, Q. / Castellino, F.J. / Geiger, J.H.
History
DepositionMay 13, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 24, 2013Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Apr 3, 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_initial_refinement_model / pdbx_struct_conn_angle / 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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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: Conantokin-G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4215
Polymers2,2651
Non-polymers1564
Water1,20767
1
A: Conantokin-G
hetero molecules

A: Conantokin-G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,84210
Polymers4,5302
Non-polymers3118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
2
A: Conantokin-G
hetero molecules

A: Conantokin-G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,84210
Polymers4,5302
Non-polymers3118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_777-y+2,-x+2,-z+5/21
Buried area1490 Å2
ΔGint-76 kcal/mol
Surface area3170 Å2
MethodPISA
3
A: Conantokin-G
hetero molecules

A: Conantokin-G
hetero molecules

A: Conantokin-G
hetero molecules

A: Conantokin-G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,68420
Polymers9,0614
Non-polymers62316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation5_757-x+2,y,-z+21
crystal symmetry operation6_567x,-y+1,-z+21
MethodPQS
Unit cell
Length a, b, c (Å)29.334, 29.334, 46.892
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-101-

CA

21A-111-

HOH

31A-142-

HOH

DetailsIn the presence of calcium, con-G forms an antiparallel dimeric structure.

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Components

#1: Protein/peptide Conantokin-G / Con-G / CGX-1007 / Conotoxin GV / Sleeper peptide


Mass: 2265.196 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The con-G peptide was synthesized. The sequence of the peptide is naturally found in Conus geographus (geography cone)
Source: (synth.) Conus geographus (geography cone) / References: UniProt: P07231
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8 / Details: 35% dioxane, pH 8, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 12427 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.081 / Χ2: 1.036 / Net I/σ(I): 7.1
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.923 / Num. unique all: 611 / Χ2: 0.353 / % possible all: 94.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT2data extraction
PHASERphasing
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 14-mer polyalanine helix

Resolution: 1.25→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.161 -Random
Rwork0.119 --
all0.121 --
obs0.119 6727 -
Displacement parametersBiso mean: 27.161 Å2
Refinement stepCycle: LAST / Resolution: 1.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms158 0 4 67 229
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d0.024

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