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- PDB-5kmf: Structure of CavAb in complex with nimodipine -

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Basic information

Entry
Database: PDB / ID: 5kmf
TitleStructure of CavAb in complex with nimodipine
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 / identical protein binding / metal ion 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
nimodipine / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 26, 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 / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)142,34621
Polymers132,3564
Non-polymers9,99017
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18250 Å2
ΔGint-175 kcal/mol
Surface area44700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.280, 125.365, 191.625
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: 33088.965 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-6U9 / nimodipine / ~{O}3-(2-methoxyethyl) ~{O}5-propan-2-yl (4~{S})-2,6-dimethyl-4-(3-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate


Mass: 418.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N2O7 / Comment: channel blocker*YM
#3: Chemical
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 5.68 Å3/Da / Density % sol: 78.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate,100uM nimodipine
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: 0.9199 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.502
11K, H, -L20.498
ReflectionResolution: 3.2→30 Å / Num. obs: 55285 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.2
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 9 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MS2

4ms2


Resolution: 3.2→29.79 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.911 / SU B: 22.014 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25572 2456 4.9 %RANDOM
Rwork0.21715 ---
obs0.21906 47933 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 105.829 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--21.29 Å20 Å2
3----21.53 Å2
Refinement stepCycle: 1 / Resolution: 3.2→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7192 0 189 12 7393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.027566
X-RAY DIFFRACTIONr_bond_other_d0.0020.027523
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.97510275
X-RAY DIFFRACTIONr_angle_other_deg1.883317172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1065872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02821.781292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.397151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0711540
X-RAY DIFFRACTIONr_chiral_restr0.0720.21226
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028004
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021856
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.31910.8413500
X-RAY DIFFRACTIONr_mcbond_other8.3213499
X-RAY DIFFRACTIONr_mcangle_it10.7416.2474368
X-RAY DIFFRACTIONr_mcangle_other10.7394369
X-RAY DIFFRACTIONr_scbond_it8.83610.5844065
X-RAY DIFFRACTIONr_scbond_other8.8354066
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.12715.8585907
X-RAY DIFFRACTIONr_long_range_B_refined10.69299.57731398
X-RAY DIFFRACTIONr_long_range_B_other10.69299.57831398
X-RAY DIFFRACTIONr_rigid_bond_restr11.35537565
X-RAY DIFFRACTIONr_sphericity_free33.65758
X-RAY DIFFRACTIONr_sphericity_bonded44.41457385
LS refinement shellResolution: 3.198→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.522 185 -
Rwork0.422 3365 -
obs--97.55 %

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