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- PDB-3v0e: Crystal structure of Ciona intestinalis voltage sensor-containing... -

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Basic information

Entry
Database: PDB / ID: 3v0e
TitleCrystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 256-576(C363S)
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 / Tyrosine specific protein phosphatases domain profile. / 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
Voltage-sensor containing phosphatase
Similarity search - Component
Biological speciesCiona intestinalis (vase tunicate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Nov 12, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,66810
Polymers36,9891
Non-polymers6799
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Voltage-sensor containing phosphatase
hetero molecules

A: Voltage-sensor containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,33520
Polymers73,9782
Non-polymers1,35818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5280 Å2
ΔGint-181 kcal/mol
Surface area29700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.849, 38.605, 89.832
Angle α, β, γ (deg.)90.00, 103.99, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Voltage-sensor containing phosphatase


Mass: 36988.895 Da / Num. of mol.: 1 / Fragment: unp residues 256-576 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.1-2.3 M ammonium sulfate, 0.1 M HEPES, pH 7.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: Oct 10, 2009 / 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: 1.6→90 Å / Num. all: 44934 / Num. obs: 43750 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.1
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.4 / % possible all: 82.2

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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 entry 1D5R

1d5r


Resolution: 1.65→87.17 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.473 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20959 2058 5 %RANDOM
Rwork0.1766 ---
obs0.17829 38746 99.05 %-
all-41193 --
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: 32.126 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å20 Å2-0.63 Å2
2--3.71 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 1.65→87.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 34 222 2826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222694
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9593652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3525336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24423.78127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58815474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1521517
X-RAY DIFFRACTIONr_chiral_restr0.080.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212033
X-RAY DIFFRACTIONr_mcbond_it0.9931.51613
X-RAY DIFFRACTIONr_mcangle_it1.79922625
X-RAY DIFFRACTIONr_scbond_it1.93431081
X-RAY DIFFRACTIONr_scangle_it3.0784.51018
X-RAY DIFFRACTIONr_rigid_bond_restr1.00732694
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 134 -
Rwork0.268 2635 -
obs--91.15 %
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)
10.1316-0.0395-0.03670.0596-0.00830.02890.00270.0095-0.0007-0.0047-0.0047-0.00280.0004-0.00250.0020.0868-0.0016-0.00290.0643-0.00170.147-14.5797.57622.863
20.01360.01680.00360.00930.003-0.0011-0.0050.00150.00080.0040.00240.00010.0016-0.00040.00260.08790-0.00060.06540.00080.1534-10.6364.87715.46
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A255 - 574
2X-RAY DIFFRACTION2A1 - 9

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