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PDB | 1T3S | Structural Analysis of the Voltage-Dependent Calcium Channel Beta Subunit Functional Core

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Internal ID
22458
PDB Entry ID
1T3S
Title
Structural Analysis of the Voltage-Dependent Calcium Channel Beta Subunit Functional Core
Authors
Opatowsky, Y.,Chen, C.-C.,Campbell, K.P.,Hirsch, J.A.
Primary Citation
AuthorsOpatowsky, Y., Chen, C.C., Campbell, K.P., Hirsch, J.A.
TitleStructural analysis of the voltage-dependent calcium channel beta subunit functional core and its complex with the alpha 1 interaction domain.
JournalNeuron, v.42, pp.387 - 399, 2004
AbstractView
Pubmed15134636
DOI10.1093/hmg/ddh162
 
History
Deposition: 2004-04-27Release: 2004-05-25Last Modified: 2014-02-12
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
2.300.2620.2610.277P 21 21 2
Unit Cell
Length [Å]a74.07b163.84c34.76
Angles [°]alpha90.00beta90.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Dihydropyridine-sensitive L-type, calcium channel beta-2 subunitP122RFunctional Core (Residues 25-422)A
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Oryctolagus cuniculusrabbitEscherichia coli BL21(DE3)
Related PDB Entries
Chemical Component
IdentifierNameFromulaLigand StructureLigand Interaction
HGMERCURY (II) IONHg2[View][View]
SCOP Classification
CATH Classification
Structural Details
Keywordtransport protein
TextSH3 DOMAIN, GUANYLATE KINASE DOMAIN, transport protein
 
Polymeric Molecules
Chain A
DescriptionDihydropyridine-sensitive L-type, calcium channel beta-2 subunit
FragmentFunctional Core (Residues 25-422)
MutationP122R
Polymer typepolypeptide
Formula Weight38341.3
Source Methodgenetically manipulated
Entity NameVoltage-Dependent Calcium Channel Beta-2 Subunit, CAB2
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aApolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
HGMERCURY (II) IONHg2200.590View
Natural/Genetically Modified Source
Common Namerabbit
Scientific NameOryctolagus cuniculus
Source GenusOryctolagus
GeneCACNB2, CACNLB2
Host Common Namen/a
Host Scientific NameEscherichia coli BL21(DE3)
Host GenusEscherichia coli BL21(DE3)
Host Cell Linen/a
Host StrainBL21(DE3)
Host Vector Typeplasmid
Host PlasmidpET21
 
Crystallization Experiments
MethodVAPOR DIFFUSION, HANGING DROP
PH9.0
Temperature292.0
DetailsPEG 20K, BICINE, SODIUM CHLORIDE, BETA-MERCAPTOETHANOL, MPD, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 292K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
74.07163.8434.76
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.0090.00
Space Group
P 21 21 2
Diffraction Detector
DetectorCCD
TypeADSC QUANTUM 4
Detailsn/a
Collection Date2002-07-15
 
Diffraction Radiation
Monochromatorn/a
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.9333
 
Diffraction Source
SourceSYNCHROTRON
TypeESRF BEAMLINE ID14-2
SiteESRF
BeamlineID14-2
 
Reflection Details
Observed Criterion Sigma (F)0.0
Observed Criterion Sigma (I)0.0
Resolution (High)2.30
Resolution (Low)50.00
Number Reflections (All) n/a
Number Reflections (Observed)18271
Percent Possible (Observed)n/a
R Merge I (Observed)0.048
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancyn/a
 
High Resolution Shell Details
Resolution(High)2.30
Resolution(Low)n/a
Percent Possible(All) 87.90
R Merge I(Observed)0.310
Mean I Over Sigma(Observed)4.3
R Sym I(Observed)n/a
Redundancyn/a
Num Unique Reflections(All)n/a
 
Refinement Statistics
Structure Solution MethodMAD
Resolution (High)2.30
Resolution (Low)81.65
Cut-off Sigma (F)n/a
Cut-off Sigma (I)n/a
Number of Reflections (All)18229
Number of Reflections (Observed)17294
Number of Reflections (R-Free) 935
Percent Reflections (Observed)92.79
R-Factor (All)n/a
R-Factor (Observed)0.26222
R-Work0.26147
R-Free0.27728
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modelisotropic
Mean Isotropic B Value57.757
Anisotropic B[1][1]-3.86
Anisotropic B[1][2]0.00
Anisotropic B[1][3]0.00
Anisotropic B[2][2]5.23
Anisotropic B[2][3]0.00
Anisotropic B[3][3]-1.37
 
Resolution Shells
Shell Resol (High)2.30
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)70
Number of Reflections (R-Work)1168
R-Factor (R-Work)0.377
R-Factor (R-Free)0.343
R-Free Errorn/a
Percent Reflections (Observed)n/a
 
RMS Deviations
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Parameter TypeDeviation From Ideal
r_bond_refined_d0.008
r_bond_other_d0.000
r_angle_refined_deg1.536
r_angle_other_deg3.506
r_dihedral_angle_1_deg1.213
r_dihedral_angle_2_degn/a
r_dihedral_angle_3_degn/a
r_dihedral_angle_4_degn/a
r_chiral_restr0.108
r_gen_planes_refined0.009
First|Previous|1 of 4|Next|Last|
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms2282
Nucleic Acid Atoms0
Heterogen Atoms1
Solvent Atoms87
 
Programs
Data Collectionn/a
Data Reduction (intensity integration)DENZO
Data Reduction (data scaling)SCALEPACK
Structure SolutionSOLVE
Structure RefinementREFMAC 5.1.24
 
Software
Classificationrefinement
Software NameREFMAC
Software Version 5.1.24
 
Sequence Chain
A
Sequence
  1   SRPSDSDVSL  EEDREAVRRE  AERQAQAQLE  KAKTKPVAFA  VRTNVSYSAA  HEDDVPVPGM

 61   AISFEAKDFL  HVKEKFNNDW  WIGRLVKEGC  EIGFIPSRVK  LENMRLQHEQ  RAKEFKLHSK

121   EKRMPFFKKT  EHTPPYDVVP  SMRPVVLVGP  SLKGYEVTDM  MQKALFDFLK  HRFEGRISIT

181   RVTADISLAK  RSVLNNPSKH  AIIERSNTRS  SLAEVQSEIE  RIFELARTLQ  LVVLDADTIN

241   HPAQLSKTSL  APIVVYVKIS  SPKVLQRLIK  SRGKSQAKHL  NVQMVAADKL  AQCPPELFDV

301   ILDENQLEDA  CEHLADYLEA  YWKATHPPSS  NLPNPLL