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- PDB-4ms2: Structural basis of Ca2+ selectivity of a voltage-gated calcium c... -

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Basic information

Entry
Database: PDB / ID: 4ms2
TitleStructural basis of Ca2+ selectivity of a voltage-gated calcium channel
ComponentsIon transport protein
KeywordsMETAL TRANSPORT / Tetrameric / Voltage-gated Ion Channel / Voltage-gated Calcium Channel / Calcium Selective / Transport protein / Membrane
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-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsTang, L. / Gamal El-Din, T.M. / Payandeh, J. / Martinez, G.Q. / Heard, T.M. / Scheuer, T. / Zheng, N. / Catterall, W.A.
CitationJournal: Nature / Year: 2014
Title: Structural basis for Ca2+ selectivity of a voltage-gated calcium channel.
Authors: Tang, L. / Gamal El-Din, T.M. / Payandeh, J. / Martinez, G.Q. / Heard, T.M. / Scheuer, T. / Zheng, N. / Catterall, W.A.
History
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Sep 20, 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 / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)123,61029
Polymers109,8304
Non-polymers13,77925
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-171 kcal/mol
Surface area45370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.790, 177.540, 131.140
Angle α, β, γ (deg.)90.00, 132.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ion transport protein


Mass: 27457.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Strain: RM4018 / Gene: Abu_1752 / Plasmid: PFASTBAC DUAL / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 38 / 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: 7.89 Å3/Da / Density % sol: 84.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: 0.1M Na-citrate, pH 4.75, 2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→40.37 Å / Num. all: 74174 / Num. obs: 74174 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.078
Reflection shellResolution: 2.75→2.9 Å / % possible all: 96.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RVY

3rvy


Resolution: 2.75→40.367 Å / SU ML: 0.36 / σ(F): 0.02 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 7245 5.03 %
Rwork0.232 --
obs0.2332 144084 94.04 %
all-72843 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→40.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7192 0 659 38 7889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128046
X-RAY DIFFRACTIONf_angle_d1.37710838
X-RAY DIFFRACTIONf_dihedral_angle_d18.6942930
X-RAY DIFFRACTIONf_chiral_restr0.0691252
X-RAY DIFFRACTIONf_plane_restr0.0071196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.78130.40341890.3473749X-RAY DIFFRACTION76
2.7813-2.8140.35911840.32713916X-RAY DIFFRACTION82
2.814-2.84830.29792490.2974359X-RAY DIFFRACTION88
2.8483-2.88430.29831940.29914381X-RAY DIFFRACTION91
2.8843-2.92230.35622290.30524653X-RAY DIFFRACTION94
2.9223-2.96230.33912820.30654626X-RAY DIFFRACTION96
2.9623-3.00460.30532250.2994574X-RAY DIFFRACTION96
3.0046-3.04940.34362770.29924762X-RAY DIFFRACTION96
3.0494-3.09710.29872550.29214598X-RAY DIFFRACTION97
3.0971-3.14780.34762360.30094757X-RAY DIFFRACTION97
3.1478-3.20210.27552770.28784708X-RAY DIFFRACTION97
3.2021-3.26030.3132690.27764634X-RAY DIFFRACTION97
3.2603-3.3230.2762370.26684672X-RAY DIFFRACTION97
3.323-3.39080.26722590.24594736X-RAY DIFFRACTION97
3.3908-3.46450.27122410.25624635X-RAY DIFFRACTION96
3.4645-3.5450.25292540.22564734X-RAY DIFFRACTION96
3.545-3.63360.25462850.22374648X-RAY DIFFRACTION97
3.6336-3.73180.2632400.22314661X-RAY DIFFRACTION96
3.7318-3.84150.19792420.19534662X-RAY DIFFRACTION96
3.8415-3.96540.2372900.18994604X-RAY DIFFRACTION96
3.9654-4.1070.18642540.1934649X-RAY DIFFRACTION96
4.107-4.27130.22342640.20084573X-RAY DIFFRACTION96
4.2713-4.46540.1972130.21024649X-RAY DIFFRACTION95
4.4654-4.70050.22142610.19524612X-RAY DIFFRACTION95
4.7005-4.99450.21332000.21074663X-RAY DIFFRACTION95
4.9945-5.37930.2681960.24994571X-RAY DIFFRACTION94
5.3793-5.91920.30762470.284554X-RAY DIFFRACTION94
5.9192-6.77220.3442470.2874525X-RAY DIFFRACTION94
6.7722-8.5190.27942480.21894560X-RAY DIFFRACTION94
8.519-40.37090.20092010.19514414X-RAY DIFFRACTION90

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