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- PDB-3v0i: Crystal structure of Ciona intestinalis voltage sensor-containing... -

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Basic information

Entry
Database: PDB / ID: 3v0i
TitleCrystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 256-576, E411F
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
Voltage-sensor containing phosphatase
Similarity search - Component
Biological speciesCiona intestinalis (vase tunicate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.1Jun 26, 2013Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4075
Polymers37,0231
Non-polymers3844
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.980, 76.590, 84.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Voltage-sensor containing phosphatase


Mass: 37023.020 Da / Num. of mol.: 1 / Fragment: unp residues 256-576 / Mutation: E411F
Source method: isolated from a genetically manipulated source
Details: His6-tag and TEV site at N-terminal / 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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5M 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: Jul 16, 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: 1.95→100 Å / Num. all: 24907 / Num. obs: 24720 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 13.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8

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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: 3V0E

3v0e


Resolution: 1.95→56.89 Å / Cor.coef. Fo:Fc: 0.8 / Cor.coef. Fo:Fc free: 0.877 / SU B: 9.882 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25927 1145 5 %RANDOM
Rwork0.21911 ---
obs0.22114 21796 92.1 %-
all-23656 --
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: 18.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.95→56.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 20 217 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222428
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9543279
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.585294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44523.805113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50715429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4931514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211812
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_it0.4211.51455
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81922357
X-RAY DIFFRACTIONr_scbond_it1.0543973
X-RAY DIFFRACTIONr_scangle_it1.7974.5920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 41 -
Rwork0.222 1084 -
obs--63.03 %
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)
11.3485-0.6318-0.50180.81820.17790.19520.05430.054-0.0099-0.0266-0.0695-0.0641-0.0294-0.02110.01520.05760.0027-0.01150.05570.00150.1885.442-9.284-20.998
20.2332-0.1368-0.1620.33530.10370.12350.00930.0053-0.03770.0086-0.02140.0468-0.02380.02150.01210.1084-0.0061-0.01640.1120.01030.14791.215-8.388-19.203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A256 - 573
2X-RAY DIFFRACTION2A601 - 604
3X-RAY DIFFRACTION2A701 - 917

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