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- PDB-4g7v: Crystal structure of voltage sensing domain of Ci-VSP with fragme... -

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Basic information

Entry
Database: PDB / ID: 4g7v
TitleCrystal structure of voltage sensing domain of Ci-VSP with fragment antibody (R217E, 2.5 A)
Components
  • (fragment antibody ...) x 2
  • Voltage-sensor containing phosphatase
KeywordsMEMBRANE PROTEIN / alpha helix / fragment antibody / voltage sensing domain / sensing voltage
Function / homology
Function and homology information


phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / dephosphorylation / monoatomic ion channel activity / membrane / cytosol
Similarity search - Function
TPTE, protein tyrosine phosphatase-like catalytic domain / 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 / Voltage-dependent channel domain superfamily / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site ...TPTE, protein tyrosine phosphatase-like catalytic domain / 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 / 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. / C2 domain superfamily / Protein-tyrosine phosphatase-like / Ion transport domain / Ion transport protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
SUCCINIC ACID / Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / Voltage-sensor containing phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
Ciona intestinalis (vase tunicate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, Q.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2014
Title: Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain.
Authors: Li, Q. / Wanderling, S. / Paduch, M. / Medovoy, D. / Singharoy, A. / McGreevy, R. / Villalba-Galea, C.A. / Hulse, R.E. / Roux, B. / Schulten, K. / Kossiakoff, A. / Perozo, E.
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: fragment antibody heavy chain
L: fragment antibody light chain
S: Voltage-sensor containing phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2078
Polymers67,3653
Non-polymers8425
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.250, 120.250, 229.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11L-301-

CL

21H-471-

HOH

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Components

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Protein , 1 types, 1 molecules S

#3: Protein Voltage-sensor containing phosphatase


Mass: 21168.658 Da / Num. of mol.: 1 / Mutation: R217E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Gene: Ci-VSP / Plasmid: pQE32 with sequence coding for Ci-VSD / Production host: Escherichia coli (E. coli) / Strain (production host): XL10-Gold / References: UniProt: Q4W8A1, UniProt: F6XHE4*PLUS

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Antibody , 2 types, 2 molecules HL

#1: Antibody fragment antibody heavy chain


Mass: 23092.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Plasmid: phagemid coding for both heavy chain and light chain of the fragment antibody
Production host: Escherichia coli (E. coli) / Strain (production host): 55244
#2: Antibody fragment antibody light chain


Mass: 23103.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Plasmid: phagemid coding for both heavy chain and light chain of the fragment antibody
Production host: Escherichia coli (E. coli) / Strain (production host): 55244

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Non-polymers , 4 types, 202 molecules

#4: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M SPG, 20% PEG 1500, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 23-ID-B1
SYNCHROTRONAPS 24-ID-E2
Detector
TypeIDDetector
MAR 300 CCD1CCD
ADSC QUANTUM 3152CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 33756 / Num. obs: 33756 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rsym value: 0.168

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Processing

Software
NameVersionClassification
JBluceat 23-IDdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→37.238 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1725 5 %Random
Rwork0.2008 ---
obs0.2028 -99.39 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.501 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5395 Å2-0 Å2-0 Å2
2--3.5395 Å2-0 Å2
3----7.0791 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4305 0 57 197 4559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084458
X-RAY DIFFRACTIONf_angle_d1.1266047
X-RAY DIFFRACTIONf_dihedral_angle_d14.5151585
X-RAY DIFFRACTIONf_chiral_restr0.074687
X-RAY DIFFRACTIONf_plane_restr0.004755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.57360.36871390.29512667X-RAY DIFFRACTION100
2.5736-2.65660.31441420.27762680X-RAY DIFFRACTION100
2.6566-2.75160.30731420.24752701X-RAY DIFFRACTION100
2.7516-2.86170.27081420.23992700X-RAY DIFFRACTION100
2.8617-2.99190.29111400.22612698X-RAY DIFFRACTION100
2.9919-3.14950.26111430.22192701X-RAY DIFFRACTION100
3.1495-3.34670.27631420.20212725X-RAY DIFFRACTION99
3.3467-3.6050.24371420.19522721X-RAY DIFFRACTION100
3.605-3.96740.23011440.19082736X-RAY DIFFRACTION99
3.9674-4.54060.21411460.16292755X-RAY DIFFRACTION99
4.5406-5.71730.1921470.16112779X-RAY DIFFRACTION98
5.7173-37.24220.20811560.20792934X-RAY DIFFRACTION98

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