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- PDB-6juh: structure of CavAb in complex with efonidipine -

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Basic information

Entry
Database: PDB / ID: 6juh
Titlestructure of CavAb in complex with efonidipine
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / voltage-gated Calcium channel block
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
Chem-C9X / SN-GLYCEROL-3-PHOSPHATE / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri RM4018 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTang, L. / Xu, F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structural basis for efonidipine block of a voltage-gated Ca2+channel.
Authors: Xu, F. / Xiong, W. / Huang, Y. / Shen, J. / Zhou, D. / Tang, L.
History
DepositionApr 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)131,19119
Polymers124,3634
Non-polymers6,82815
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26390 Å2
ΔGint-228 kcal/mol
Surface area53220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.860, 125.520, 191.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ion transport protein


Mass: 31090.836 Da / Num. of mol.: 4 / Mutation: E1177D, S1178D, M1181N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri RM4018 (bacteria) / Strain: RM4018 / Variant: RM4018 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5

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Non-polymers , 5 types, 15 molecules

#2: Chemical
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#3: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#4: Chemical
ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9O6P
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Ca
#6: Chemical ChemComp-C9X / 2-[phenyl-(phenylmethyl)amino]ethyl (4~{R})-5-(5,5-dimethyl-2-oxidanylidene-1,3,2$l^{5}-dioxaphosphinan-2-yl)-2,6-dimethyl-4-(3-nitrophenyl)-1,4-dihydropyridine-3-carboxylate


Mass: 631.655 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C34H38N3O7P

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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: 6.11 Å3/Da / Density % sol: 79.86 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 1.0-2.0M Ammonium Sulfate 100 mM Na-citrate pH=5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 53912 / % possible obs: 89 % / Redundancy: 5 % / Net I/σ(I): 9.6
Reflection shellResolution: 3→3.16 Å / Num. unique obs: 8310

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Processing

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

4ms2


Resolution: 3→29.818 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.84
RfactorNum. reflection% reflection
Rfree0.2907 2663 4.94 %
Rwork0.2349 --
obs0.2377 53911 88.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→29.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8640 0 211 0 8851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119053
X-RAY DIFFRACTIONf_angle_d1.43512290
X-RAY DIFFRACTIONf_dihedral_angle_d19.1253215
X-RAY DIFFRACTIONf_chiral_restr0.0821464
X-RAY DIFFRACTIONf_plane_restr0.0071462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.05450.40161140.33412877X-RAY DIFFRACTION94
3.0545-3.11320.38671370.31132819X-RAY DIFFRACTION95
3.1132-3.17670.31361540.30372875X-RAY DIFFRACTION95
3.1767-3.24570.3451530.28022837X-RAY DIFFRACTION95
3.2457-3.32110.28841420.2462860X-RAY DIFFRACTION95
3.3211-3.4040.26971390.22012844X-RAY DIFFRACTION94
3.404-3.49590.2476870.22751756X-RAY DIFFRACTION58
3.4959-3.59860.33481450.222848X-RAY DIFFRACTION94
3.5986-3.71460.29191090.23651908X-RAY DIFFRACTION64
3.7146-3.84710.24211570.21832843X-RAY DIFFRACTION94
3.8471-4.00080.29351050.20762115X-RAY DIFFRACTION70
4.0008-4.18240.29991480.21572841X-RAY DIFFRACTION93
4.1824-4.40220.26771540.212818X-RAY DIFFRACTION93
4.4022-4.67710.24621490.19882833X-RAY DIFFRACTION93
4.6771-5.03660.27361490.20132832X-RAY DIFFRACTION93
5.0366-5.54050.30581550.23112815X-RAY DIFFRACTION92
5.5405-6.33560.35811450.2812837X-RAY DIFFRACTION92
6.3356-7.95690.28811410.27262819X-RAY DIFFRACTION90
7.9569-29.81970.28051800.23232871X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: -3.327 Å / Origin y: 30.9757 Å / Origin z: 32.4806 Å
111213212223313233
T0.357 Å2-0.007 Å2-0.0222 Å2-0.3743 Å20.0146 Å2--0.357 Å2
L0.3169 °2-0.0049 °2-0.0544 °2-0.2123 °2-0.0278 °2--0.5289 °2
S0.0273 Å °-0.1163 Å °-0.0179 Å °0.0836 Å °0.0019 Å °-0.0104 Å °-0.0474 Å °-0.0298 Å °0 Å °
Refinement TLS groupSelection details: all

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