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- PDB-3v0h: Crystal structure of Ciona intestinalis voltage sensor-containing... -

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Basic information

Entry
Database: PDB / ID: 3v0h
TitleCrystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 241-576(C363S), complexed with D-MYO-inositol-1,4,5-triphosphate
ComponentsVoltage-sensor containing phosphatase
KeywordsHYDROLASE / PTP / C2 / Phosphatase
Function / homology
Function and homology information


phosphatase activity / monoatomic ion channel activity / membrane
Similarity search - Function
TPTE, protein tyrosine phosphatase-like catalytic domain / : / Immunoglobulin-like - #1110 / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Polymorphic toxin system, DSP-PTPase phosphatase ...TPTE, protein tyrosine phosphatase-like catalytic domain / : / Immunoglobulin-like - #1110 / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Polymorphic toxin system, DSP-PTPase phosphatase / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Voltage-dependent channel domain superfamily / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / C2 domain superfamily / Ion transport domain / Ion transport protein / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Voltage-sensor containing phosphatase
Similarity search - Component
Biological speciesCiona intestinalis (vase tunicate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLiu, L. / Kohout, S.C. / Xu, Q. / Muller, S. / Kimberlin, C. / Isacoff, E.Y. / Minor, D.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A glutamate switch controls voltage-sensitive phosphatase function.
Authors: Liu, L. / Kohout, S.C. / Xu, Q. / Muller, S. / Kimberlin, C.R. / Isacoff, E.Y. / Minor, D.L.
History
DepositionDec 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Voltage-sensor containing phosphatase
B: Voltage-sensor containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3366
Polymers77,6562
Non-polymers1,6804
Water12,160675
1
A: Voltage-sensor containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6683
Polymers38,8281
Non-polymers8402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Voltage-sensor containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6683
Polymers38,8281
Non-polymers8402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.665, 79.852, 87.927
Angle α, β, γ (deg.)90.00, 92.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Voltage-sensor containing phosphatase


Mass: 38827.984 Da / Num. of mol.: 2 / Fragment: unp residues 241-576 / Mutation: C363S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Gene: Ci-VSP / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 pLysS / References: UniProt: Q4W8A1
#2: Chemical
ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17.5-22.5% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl, pH 8.0; complex was made by soaking method, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2010 / Details: Double Crystal Si(111)
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.85→89 Å / Num. all: 59900 / Num. obs: 59840 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 17.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 3V0D

3v0d


Resolution: 1.85→87.85 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.903 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22229 3021 5.1 %RANDOM
Rwork0.18068 ---
obs0.18279 56716 99.9 %-
all-56728 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å2-0.09 Å2
2--0.65 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.85→87.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5266 0 96 675 6037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225652
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9717687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7095703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11723.835279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.028151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7921540
X-RAY DIFFRACTIONr_chiral_restr0.0810.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214268
X-RAY DIFFRACTIONr_mcbond_it0.5381.53320
X-RAY DIFFRACTIONr_mcangle_it1.05425408
X-RAY DIFFRACTIONr_scbond_it1.49632332
X-RAY DIFFRACTIONr_scangle_it2.4884.52253
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 220 -
Rwork0.239 4158 -
obs--99.64 %
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)
10.84970.3803-0.50730.2827-0.46310.8330.03520.0074-0.07290.1017-0.0701-0.0341-0.1967-0.0020.03490.1650.0213-0.00160.117-0.01910.08677.033-3.74434.752
20.79150.0475-0.44690.04920.02760.5357-0.03110.0173-0.01740.00660.00880.0158-0.0632-0.00510.02230.14-0.00740.01690.09540.00610.125210.885.267-9.095
30.10020.0868-0.15760.0905-0.11260.4014-0.02470.0020.00040.018-0.0028-0.0167-0.03680.00310.02750.1460.01650.00190.1142-0.00820.11488.891-0.18313.47
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A250 - 575
2X-RAY DIFFRACTION1A1 - 2
3X-RAY DIFFRACTION2B249 - 575
4X-RAY DIFFRACTION2B3 - 4
5X-RAY DIFFRACTION3A5 - 237
6X-RAY DIFFRACTION3A577 - 765
7X-RAY DIFFRACTION3B577 - 827

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