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- PDB-5klb: Crystal structure of the CavAb voltage-gated calcium channel(wild... -

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Basic information

Entry
Database: PDB / ID: 5klb
TitleCrystal structure of the CavAb voltage-gated calcium channel(wild-type, 2.7A)
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / Voltage-gated Calcium Channel
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function
Voltage-gated potassium channels. Chain C / Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTang, L. / Gamal EL-Din, T.M. / Swanson, T.M. / Pryde, D.C. / Scheuer, T. / Zheng, N. / Catterall, W.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL112808 United States
National Research Service AwardT32GM008268 United States
CitationJournal: Nature / Year: 2016
Title: Structural basis for inhibition of a voltage-gated Ca(2+) channel by Ca(2+) antagonist drugs.
Authors: Tang, L. / El-Din, T.M. / Swanson, T.M. / Pryde, D.C. / Scheuer, T. / Zheng, N. / Catterall, W.A.
History
DepositionJun 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,81633
Polymers132,4484
Non-polymers17,36829
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45350 Å2
ΔGint-347 kcal/mol
Surface area51460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.900, 125.700, 191.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
Ion transport protein


Mass: 33112.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria)
Strain: RM4018 / Gene: Abu_1752 / Plasmid: pFASTBAC DUAL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate
PH range: 4.7-5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 770488 / % possible obs: 92.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2.4 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MS2

4ms2


Resolution: 2.7→29.932 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 7331 4.96 %
Rwork0.2191 --
obs0.2212 147876 92.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8780 0 887 17 9684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139874
X-RAY DIFFRACTIONf_angle_d1.61313340
X-RAY DIFFRACTIONf_dihedral_angle_d20.7613636
X-RAY DIFFRACTIONf_chiral_restr0.0681578
X-RAY DIFFRACTIONf_plane_restr0.0061482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6997-2.73030.37792710.31694928X-RAY DIFFRACTION97
2.7303-2.76240.4022660.30854963X-RAY DIFFRACTION98
2.7624-2.79610.37152990.29464907X-RAY DIFFRACTION98
2.7961-2.83150.32942910.27894931X-RAY DIFFRACTION98
2.8315-2.86870.31022740.26844916X-RAY DIFFRACTION98
2.8687-2.9080.28911880.24765002X-RAY DIFFRACTION97
2.908-2.94950.29532980.24274879X-RAY DIFFRACTION98
2.9495-2.99350.32452450.26034940X-RAY DIFFRACTION97
2.9935-3.04020.29043290.26644881X-RAY DIFFRACTION97
3.0402-3.090.29552490.25074918X-RAY DIFFRACTION98
3.09-3.14320.27292850.24074963X-RAY DIFFRACTION97
3.1432-3.20030.29122260.24194893X-RAY DIFFRACTION97
3.2003-3.26180.29062240.24014981X-RAY DIFFRACTION97
3.2618-3.32830.22942610.22724873X-RAY DIFFRACTION97
3.3283-3.40060.23222310.19664953X-RAY DIFFRACTION97
3.4006-3.47950.29011380.19952778X-RAY DIFFRACTION55
3.4795-3.56640.24272430.20884871X-RAY DIFFRACTION96
3.5664-3.66270.23992360.21164751X-RAY DIFFRACTION96
3.6627-3.77030.29511610.20653280X-RAY DIFFRACTION96
3.7703-3.89170.21792650.19314828X-RAY DIFFRACTION96
3.8917-4.03050.22441360.18563489X-RAY DIFFRACTION68
4.0305-4.19150.22722510.19844811X-RAY DIFFRACTION95
4.1915-4.38170.24332250.19934842X-RAY DIFFRACTION95
4.3817-4.61190.21332420.18464775X-RAY DIFFRACTION94
4.6119-4.89970.23542850.18784787X-RAY DIFFRACTION95
4.8997-5.27610.25812590.20474740X-RAY DIFFRACTION94
5.2761-5.80350.29862450.24344738X-RAY DIFFRACTION94
5.8035-6.63530.2882590.26274668X-RAY DIFFRACTION92
6.6353-8.32990.22812480.21864650X-RAY DIFFRACTION92
8.3299-29.93330.25272010.20864609X-RAY DIFFRACTION90

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