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- PDB-2rfa: Crystal structure of the mouse TRPV6 ankyrin repeat domain -

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Basic information

Entry
Database: PDB / ID: 2rfa
TitleCrystal structure of the mouse TRPV6 ankyrin repeat domain
ComponentsTransient receptor potential cation channel subfamily V member 6
KeywordsMEMBRANE PROTEIN / TRPV6 / ankyrin reapeat / transient receptor potential / ANK repeat / Calcium channel / Calcium transport / Calmodulin-binding / Glycoprotein / Ion transport / Ionic channel / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


parathyroid hormone secretion / TRP channels / calcium ion import / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / response to calcium ion / calcium ion transport ...parathyroid hormone secretion / TRP channels / calcium ion import / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / response to calcium ion / calcium ion transport / protein homotetramerization / calmodulin binding / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 6 / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Transient receptor potential cation channel subfamily V member 6 / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsPhelps, C.B. / Huang, R.J. / Wang, R.R. / Gaudet, R.
CitationJournal: Biochemistry / Year: 2008
Title: Structural analyses of the ankyrin repeat domain of TRPV6 and related TRPV ion channels.
Authors: Phelps, C.B. / Huang, R.J. / Lishko, P.V. / Wang, R.R. / Gaudet, R.
History
DepositionSep 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 6


Theoretical massNumber of molelcules
Total (without water)25,7081
Polymers25,7081
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.762, 63.045, 116.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transient receptor potential cation channel subfamily V member 6 / TrpV6 / Epithelial calcium channel 2 / ECaC2 / Calcium transport protein 1 / CaT1


Mass: 25707.594 Da / Num. of mol.: 1 / Fragment: Ankyrin Repeat Domain (residues 44-265)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpv6 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: Q91WD2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M NaHEPES, 0.1M K/Na Tartrate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.7→8 Å / Num. obs: 25172 / % possible obs: 99.08 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Biso Wilson estimate: 40.7 Å2 / Rsym value: 0.044 / Net I/σ(I): 18
Reflection shellResolution: 1.7→1.742 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1586 / Rsym value: 0.445 / % possible all: 95.34

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.3.0037refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→7.99 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.088 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1272 5.1 %RANDOM
Rwork0.168 ---
obs0.17 25172 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 0 227 1949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221790
X-RAY DIFFRACTIONr_bond_other_d0.0010.021172
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9662437
X-RAY DIFFRACTIONr_angle_other_deg0.95532889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1715233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32724.68479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.99415311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.129158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02342
X-RAY DIFFRACTIONr_nbd_refined0.2260.2448
X-RAY DIFFRACTIONr_nbd_other0.190.21335
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2902
X-RAY DIFFRACTIONr_nbtor_other0.0870.2914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2159
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1760.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.237
X-RAY DIFFRACTIONr_mcbond_it1.0821.51458
X-RAY DIFFRACTIONr_mcbond_other0.2331.5457
X-RAY DIFFRACTIONr_mcangle_it1.24821805
X-RAY DIFFRACTIONr_scbond_it2.2253740
X-RAY DIFFRACTIONr_scangle_it3.284.5627
LS refinement shellResolution: 1.7→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 92 -
Rwork0.241 1586 -
all-1678 -
obs--95.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
129.6916-0.6272-6.424537.9335-27.488147.4547-0.1048-2.7287-1.81553.30620.14691.0742.822-0.4677-0.04210.9137-0.09570.1290.15610.09640.265432.553925.806411.7263
27.16550.2476-5.69894.3803-0.87218.5584-0.43480.7578-0.5896-0.53620.13330.36281.1708-0.60720.30150.1339-0.02730.0087-0.0405-0.01080.030232.414732.12633.1561
35.69-1.2104-0.16542.52441.04923.69980.04060.065-0.0639-0.3012-0.14740.08210.09020.06580.1068-0.09790.0023-0.0077-0.10480.0103-0.057231.000541.25896.748
42.5275-0.2209-0.56622.7010.46983.54430.0511-0.1266-0.16090.0347-0.05920.1215-0.0837-0.05160.0081-0.1332-0.0054-0.0163-0.0638-0.0112-0.031626.151947.813413.7956
518.28233.9926-0.599222.4143-9.645629.45130.2564-1.6679-1.50241.3225-0.5178-0.28011.239-0.11660.26130.0634-0.05210.02640.0320.11830.045324.031549.055830.5915
61.9969-0.5751-0.99552.06791.81864.80460.0757-0.09980.1941-0.2295-0.0720.0717-0.5441-0.0151-0.0038-0.0549-0.0164-0.0084-0.1002-0.0377-0.045425.213559.798218.0067
73.22083.5703-3.014316.0431-0.07713.99120.1733-0.3680.0246-0.24110.0714-0.905-0.35450.5553-0.2447-0.1367-0.06420.00910.003-0.11720.019730.671765.287724.0611
820.5573-3.0105-10.672624.9123.266430.92180.82492.03862.2781-2.9551-0.41581.0608-2.188-2.03-0.4090.53110.2052-0.08440.20960.09920.404316.678273.797819.1537
98.61163.5045.00674.8813.13245.45850.2056-0.18910.19930.2531-0.34930.3083-0.1003-0.18930.1436-0.0848-0.02240.05690.0536-0.13470.013621.610266.425633.3597
1025.62830.53765.147563.717-16.30365.2618-0.63120.33233.4114-0.26440.4745-0.9901-0.2313-0.9970.15670.10060.10450.0490.28590.01760.392324.969378.054531.0209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA44 - 482 - 6
2X-RAY DIFFRACTION2AA49 - 777 - 35
3X-RAY DIFFRACTION3AA78 - 10736 - 65
4X-RAY DIFFRACTION4AA108 - 15366 - 111
5X-RAY DIFFRACTION5AA154 - 162112 - 120
6X-RAY DIFFRACTION6AA163 - 204121 - 162
7X-RAY DIFFRACTION7AA205 - 223163 - 181
8X-RAY DIFFRACTION8AA224 - 233182 - 191
9X-RAY DIFFRACTION9AA234 - 257192 - 215
10X-RAY DIFFRACTION10AA258 - 265216 - 223

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