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- PDB-3v0g: Crystal structure of Ciona intestinalis voltage sensor-containing... -

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Basic information

Entry
Database: PDB / ID: 3v0g
TitleCrystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 241-576(C363S), form III
ComponentsVoltage-sensor containing phosphatase
KeywordsHYDROLASE / PTP / C2 / Phosphatase
Function / homology
Function and homology information


protein tyrosine phosphatase activity / ion channel activity / integral component of membrane
Similarity search - Function
Immunoglobulin-like - #1110 / Tensin phosphatase, C2 domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Tensin-type phosphatase domain / C2 tensin-type domain profile. / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Voltage-dependent channel domain superfamily ...Immunoglobulin-like - #1110 / Tensin phosphatase, C2 domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Tensin-type phosphatase domain / C2 tensin-type domain profile. / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Voltage-dependent channel domain superfamily / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 protein / Ion transport domain / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Voltage-sensor containing phosphatase
Similarity search - Component
Biological speciesCiona intestinalis (vase tunicate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

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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
C: Voltage-sensor containing phosphatase
D: Voltage-sensor containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,16713
Polymers155,3124
Non-polymers8559
Water21,0601169
1
A: Voltage-sensor containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9232
Polymers38,8281
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Voltage-sensor containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1134
Polymers38,8281
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Voltage-sensor containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1134
Polymers38,8281
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Voltage-sensor containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0183
Polymers38,8281
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)50.863, 83.863, 83.604
Angle α, β, γ (deg.)86.55, 89.55, 89.38
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Voltage-sensor containing phosphatase


Mass: 38827.984 Da / Num. of mol.: 4 / 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1169 / 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: 46.33 %
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; crystals were dehydrated in 30% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl,pH 8.0, VAPOR ...Details: 17.5-22.5% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl,pH 8.0; crystals were dehydrated in 30% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl,pH 8.0, 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: 1.5→83.8 Å / Num. all: 220438 / Num. obs: 176659 / % possible obs: 80.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.3
Reflection shellResolution: 1.5→1.5 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.4 / % possible all: 83.1

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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
Resolution: 1.6→83.71 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.882 / SU B: 3.119 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29839 7438 5.1 %RANDOM
Rwork0.25592 ---
obs0.25809 138269 80.07 %-
all-172685 --
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: 24.766 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å20.42 Å20.34 Å2
2--0.59 Å2-0.15 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.6→83.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10548 0 45 1169 11762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02210967
X-RAY DIFFRACTIONr_angle_refined_deg0.9561.95214826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28651351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90823.65537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28151960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6981578
X-RAY DIFFRACTIONr_chiral_restr0.0660.21582
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218336
X-RAY DIFFRACTIONr_mcbond_it0.3781.56559
X-RAY DIFFRACTIONr_mcangle_it0.68210648
X-RAY DIFFRACTIONr_scbond_it0.80634408
X-RAY DIFFRACTIONr_scangle_it1.2684.54154
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 550 -
Rwork0.316 10686 -
obs--83.44 %

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