[English] 日本語
Yorodumi
- PDB-6x25: CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x25
TitleCRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AFTER ADDITION OF INOSITOL 1,3,4-TRISPHOSPHATE AND LITHIUM AT 3.2 ANGSTROM RESOLUTION
ComponentsInositol polyphosphate 1-phosphatase
KeywordsSIGNALING PROTEIN / inositol phosphate / neurological disease / Bipolar disorder / manic depressive illness / phosphatase / lithium binding site
Function / homology
Function and homology information


inositol-1,3,4-trisphosphate 1-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol-1,4-bisphosphate 1-phosphatase / inositol-1,4-bisphosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / metal ion binding
Similarity search - Function
Inositol polyphosphate 1-phosphatase, domain 1 / : / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family
Similarity search - Domain/homology
GADOLINIUM ATOM / Inositol polyphosphate 1-phosphatase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 3.2 Å
AuthorsDollins, D.E. / Endo-Streeter, S. / Ren, Y. / York, J.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL055672 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124404 United States
Howard Hughes Medical Institute (HHMI)York Investigator United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A structural basis for lithium and substrate binding of an inositide phosphatase.
Authors: Dollins, D.E. / Xiong, J.P. / Endo-Streeter, S. / Anderson, D.E. / Bansal, V.S. / Ponder, J.W. / Ren, Y. / York, J.D.
History
DepositionMay 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inositol polyphosphate 1-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4845
Polymers43,9771
Non-polymers5074
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.640, 51.640, 143.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Inositol polyphosphate 1-phosphatase / IPPase


Mass: 43976.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: INPP1 / Production host: Baculoviridae sp. (virus)
References: UniProt: P21327, inositol-1,4-bisphosphate 1-phosphatase
#2: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: Tetragonal shaped crystals amenable to diffraction studies were grown by the hanging drop vapor diffusion method on silanized glass covers slips at 20 C and grew with dimensions routinely ...Details: Tetragonal shaped crystals amenable to diffraction studies were grown by the hanging drop vapor diffusion method on silanized glass covers slips at 20 C and grew with dimensions routinely exceeding 0.1 x 0.1 x 0.5mm. Gd3+, a competitive inhibitor of Mg2+, has a useful anomalous absorption edge at the CuK wavelength and therefore was used in the co-crystallization or soaking conditions. -Mg2+/+Li+/+Ins(1,3,4)P3/+Gd3+ (data=ip7r): Reservoir solution consisted of 10% PEG 8000, 80mM Bis-Tris, pH 5.25, 2mM Gd2(SO4)3, 1mM Ins(1,3,4)P3; 200mM Li2SO4

-
Data collection

DiffractionMean temperature: 296 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Aug 9, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 3.2→10.22 Å / Num. obs: 11374 / % possible obs: 85 % / Redundancy: 2.1 % / Rsym value: 0.103 / Net I/σ(I): 3.8
Reflection shellResolution: 3.2→3.45 Å / Num. unique obs: 950 / Rsym value: 0.193

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
UCSD-systemdata reduction
UCSD-systemdata scaling
SQUASHphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1INP

1inp


Resolution: 3.2→10.22 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.87 / SU B: 53.751 / SU ML: 0.428 / Cross valid method: THROUGHOUT / ESU R Free: 0.557 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24551 340 5.8 %RANDOM
Rwork0.19883 ---
obs0.20161 5527 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.415 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.76 Å20 Å2
3----1.52 Å2
Refinement stepCycle: 1 / Resolution: 3.2→10.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 12 16 2564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132592
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172467
X-RAY DIFFRACTIONr_angle_refined_deg1.041.6283509
X-RAY DIFFRACTIONr_angle_other_deg0.991.5735729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07123.902123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95215459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4381511
X-RAY DIFFRACTIONr_chiral_restr0.0260.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022841
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02500
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_it0.5473.7191300
X-RAY DIFFRACTIONr_mcbond_other0.5473.7171299
X-RAY DIFFRACTIONr_mcangle_it1.0415.8341615
X-RAY DIFFRACTIONr_mcangle_other1.0415.8371616
X-RAY DIFFRACTIONr_scbond_it0.2213.8191292
X-RAY DIFFRACTIONr_scbond_other0.1983.7831285
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4715.9221882
X-RAY DIFFRACTIONr_long_range_B_refined3.66124.9332638
X-RAY DIFFRACTIONr_long_range_B_other3.38824.9222636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.275 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 15 -
Rwork0.274 291 -
obs--75.37 %
Refinement TLS params.Method: refined / Origin x: -13.8069 Å / Origin y: 9.8218 Å / Origin z: 34.8989 Å
111213212223313233
T0.0663 Å20.0023 Å2-0.043 Å2-0.0532 Å2-0.0121 Å2--0.081 Å2
L1.278 °2-0.795 °20.3131 °2-0.8846 °20.0402 °2--2.5791 °2
S0.0984 Å °0.1247 Å °-0.1512 Å °0.069 Å °-0.0726 Å °0.0036 Å °-0.1068 Å °0.0871 Å °-0.0258 Å °

+
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