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- PDB-5cbf: Structural and Functional Characterization of a Calcium-activated... -

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Basic information

Entry
Database: PDB / ID: 5cbf
TitleStructural and Functional Characterization of a Calcium-activated Cation channel from Tsukamurella Paurometabola
ComponentsIon transport 2 domain protein
KeywordsTRANSPORT PROTEIN / membrane protein / calcium activated non-selective ion channel / 2TM helix ion channel family / tetrameric cation channel / ion transport
Function / homologyHelix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / membrane / metal ion binding / Ion transport 2 domain protein
Function and homology information
Biological speciesTsukamurella paurometabola
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.61 Å
AuthorsDhakshnamoorthy, B. / Rohaim, A. / Rui, H. / Blachowicz, L. / Roux, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM062342 United States
CitationJournal: Nat Commun / Year: 2016
Title: Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola.
Authors: Dhakshnamoorthy, B. / Rohaim, A. / Rui, H. / Blachowicz, L. / Roux, B.
History
DepositionJun 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Mar 7, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Dec 25, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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 2 domain protein
B: Ion transport 2 domain protein
C: Ion transport 2 domain protein
D: Ion transport 2 domain protein
E: Ion transport 2 domain protein
F: Ion transport 2 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8319
Polymers84,7116
Non-polymers1203
Water00
1
A: Ion transport 2 domain protein
B: Ion transport 2 domain protein
D: Ion transport 2 domain protein
E: Ion transport 2 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5947
Polymers56,4744
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-145 kcal/mol
Surface area17780 Å2
MethodPISA
2
C: Ion transport 2 domain protein


Theoretical massNumber of molelcules
Total (without water)14,1181
Polymers14,1181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6930 Å2
MethodPISA
3
F: Ion transport 2 domain protein


Theoretical massNumber of molelcules
Total (without water)14,1181
Polymers14,1181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.053, 116.053, 132.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 5 - 106 / Label seq-ID: 5 - 106

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
DetailsSEC-MALS indicates that the biological assembly is a tetramer.

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Components

#1: Protein
Ion transport 2 domain protein


Mass: 14118.424 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tsukamurella paurometabola (strain ATCC 8368 / DSM 20162 / JCM 10117 / NBRC 16120 / NCTC 13040) (bacteria)
Strain: ATCC 8368 / DSM 20162 / JCM 10117 / NBRC 16120 / NCTC 13040
Gene: Tpau_1687 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue / References: UniProt: D5UM26
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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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: 2.63 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 200, cacodylate, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97902 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionRedundancy: 4.8 % / Number: 47646 / Rmerge(I) obs: 0.145 / Χ2: 0.85 / D res high: 3.6 Å / D res low: 50 Å / Num. obs: 10003 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
9.755010.0511.5164.7
7.759.7510.0981.6535
6.777.7510.141.5355.1
6.156.7710.1820.8325.1
5.716.1510.2020.7354.3
5.385.7110.2510.6734.8
5.115.3810.2470.7374.9
4.895.1110.2210.8925
4.74.8910.22315
4.544.710.2570.7855.1
4.394.5410.2630.8595.2
4.274.3910.3090.8215.2
4.164.2710.4130.7135.1
4.054.1610.4130.6634.1
3.964.0510.390.6994.2
3.883.9610.5830.5754.6
3.83.8810.6140.5384.5
3.733.810.6260.5354.6
3.663.7310.7260.4924.5
3.63.6610.940.4614.4
ReflectionResolution: 3.6→50 Å / Num. obs: 10003 / % possible obs: 99.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 2.7
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 4.4 % / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CBG

5cbg


Resolution: 3.61→50 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.888 / SU B: 31.295 / SU ML: 0.486 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.715
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.279 489 4.9 %RANDOM
Rwork0.239 ---
obs0.241 9567 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 3.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 3 0 4623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024722
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2311.9646450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3315606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29421.304138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.44215738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0171524
X-RAY DIFFRACTIONr_chiral_restr0.1720.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213366
X-RAY DIFFRACTIONr_gen_planes_other
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_it8.96511.492442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it14.50617.2293042
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.35511.4112280
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2480.18
12B2480.18
21A2560.22
22C2560.22
31A2560.19
32D2560.19
41A2500.19
42E2500.19
51A2560.16
52F2560.16
61B2480.15
62C2480.15
71B2480.18
72D2480.18
81B2560.15
82E2560.15
91B2540.15
92F2540.15
101C2540.15
102D2540.15
111C2540.18
112E2540.18
121C2620.12
122F2620.12
131D2540.16
132E2540.16
141D2580.16
142F2580.16
151E2480.15
152F2480.15
LS refinement shellResolution: 3.61→3.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 38 -
Rwork0.231 625 -
obs--89.59 %

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