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- PDB-5klg: Structure of CavAb(W195Y) in complex with Br-dihydropyridine deri... -

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Basic information

Entry
Database: PDB / ID: 5klg
TitleStructure of CavAb(W195Y) in complex with Br-dihydropyridine derivative UK-59811
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
Chem-6UC / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Atomic model / 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)140,85619
Polymers132,3564
Non-polymers8,50015
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17780 Å2
ΔGint-180 kcal/mol
Surface area45280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.915, 126.030, 192.120
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-6UC / O3-ethyl O5-methyl (4R)-4-(2-bromophenyl)-2-[2-(dimethylamino)ethoxymethyl]-6-methyl-1,4-dihydropyridine-3,5-dicarboxylate


Mass: 481.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29BrN2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 5.76 Å3/Da / Density % sol: 78.64 %
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: 0.9199 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 46609 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Net I/σ(I): 13.4
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 3.3 / Num. unique all: 46652 / % possible all: 100

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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: 3.3→29.938 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0.22 / Phase error: 32.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3029 4494 5.07 %
Rwork0.279 --
obs0.2803 88694 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→29.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7192 0 205 3 7400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137586
X-RAY DIFFRACTIONf_angle_d1.86410312
X-RAY DIFFRACTIONf_dihedral_angle_d16.7862620
X-RAY DIFFRACTIONf_chiral_restr0.1391233
X-RAY DIFFRACTIONf_plane_restr0.011209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2997-3.33720.37961460.34372755X-RAY DIFFRACTION98
3.3372-3.37640.39671460.31962868X-RAY DIFFRACTION100
3.3764-3.41750.32471500.31222810X-RAY DIFFRACTION100
3.4175-3.46070.35351120.31472779X-RAY DIFFRACTION100
3.4607-3.50620.27781300.30772869X-RAY DIFFRACTION100
3.5062-3.55420.36651400.30362798X-RAY DIFFRACTION100
3.5542-3.60480.34351460.28992843X-RAY DIFFRACTION100
3.6048-3.65860.30551460.2982798X-RAY DIFFRACTION100
3.6586-3.71560.30991320.29592877X-RAY DIFFRACTION100
3.7156-3.77640.30221560.29112727X-RAY DIFFRACTION100
3.7764-3.84140.37531360.28282876X-RAY DIFFRACTION100
3.8414-3.91110.30711760.25012799X-RAY DIFFRACTION100
3.9111-3.98620.24621760.24232727X-RAY DIFFRACTION100
3.9862-4.06740.27431580.25632840X-RAY DIFFRACTION100
4.0674-4.15560.26721670.28552750X-RAY DIFFRACTION100
4.1556-4.2520.35161420.28522864X-RAY DIFFRACTION100
4.252-4.3580.36711350.28392824X-RAY DIFFRACTION100
4.358-4.47550.28821420.27742800X-RAY DIFFRACTION100
4.4755-4.60670.32521660.26922798X-RAY DIFFRACTION100
4.6067-4.75480.26711740.27362739X-RAY DIFFRACTION100
4.7548-4.9240.28961940.26292774X-RAY DIFFRACTION100
4.924-5.12030.24871340.26592858X-RAY DIFFRACTION100
5.1203-5.3520.32521320.28692828X-RAY DIFFRACTION100
5.352-5.63250.36381590.29072779X-RAY DIFFRACTION100
5.6325-5.98270.34011230.29732869X-RAY DIFFRACTION100
5.9827-6.44040.37431620.3222759X-RAY DIFFRACTION100
6.4404-7.08080.35711900.29332806X-RAY DIFFRACTION100
7.0808-8.08770.2221200.25752806X-RAY DIFFRACTION100
8.0877-10.12370.21321680.23912791X-RAY DIFFRACTION100
10.1237-29.93940.29271360.27882789X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 187.5598 Å / Origin y: 31.259 Å / Origin z: 23.593 Å
111213212223313233
T0.6891 Å2-0.0861 Å20.0019 Å2-0.6275 Å2-0.0274 Å2--0.3 Å2
L1.9929 °2-0.087 °2-0.0104 °2-1.237 °2-0.0957 °2--1.5605 °2
S0.1669 Å °-0.6604 Å °0.0849 Å °0.3626 Å °0.0057 Å °-0.0077 Å °-0.1621 Å °-0.0113 Å °-0.0917 Å °
Refinement TLS groupSelection details: all

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