[English] 日本語
Yorodumi
- PDB-3v0g: Crystal structure of Ciona intestinalis voltage sensor-containing... -

+
Open data


ID or keywords:

Loading...

-
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


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
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 1169 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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: 1.6→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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more