[English] 日本語
Yorodumi
- PDB-6rxe: Crystal Structure of Bifidobacterium longum Multiple Inositol Pol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rxe
TitleCrystal Structure of Bifidobacterium longum Multiple Inositol Polyphosphate Phosphatase Complex with Inositol Hexasulfate
ComponentsHistidine acid phosphatase
KeywordsHYDROLASE / phytase / histidine phosphatase / MINPP / Bifidobacterium
Function / homology
Function and homology information


multiple inositol-polyphosphate phosphatase / 2,3-bisphosphoglycerate 3-phosphatase / hydrolase activity / metal ion binding / membrane
Similarity search - Function
Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
D-MYO-INOSITOL-HEXASULPHATE / PHOSPHATE ION / Multiple inositol polyphosphate phosphatase 1
Similarity search - Component
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsAcquistapace, I.M. / Brearley, C.A. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M022978/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Snapshots during the catalytic cycle of a histidine acid phytase reveal an induced-fit structural mechanism.
Authors: Acquistapace, I.M. / Zi Etek, M.A. / Li, A.W.H. / Salmon, M. / Kuhn, I. / Bedford, M.R. / Brearley, C.A. / Hemmings, A.M.
History
DepositionJun 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histidine acid phosphatase
B: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6676
Polymers112,1562
Non-polymers1,5114
Water25,8151433
1
A: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8343
Polymers56,0781
Non-polymers7562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8343
Polymers56,0781
Non-polymers7562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.829, 106.411, 76.462
Angle α, β, γ (deg.)90.00, 112.64, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Histidine acid phosphatase


Mass: 56078.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria)
Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Gene: Blon_0263 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 (DE3) pLysS / References: UniProt: B7GTV0
#2: Chemical ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O24S6
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1433 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.1 % / Description: large needle
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 10 mM HEPES, 75 mM NaCl, 10% (w/v) PEG 1000, 10% (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.84→70.57 Å / Num. obs: 90353 / % possible obs: 99.7472 % / Redundancy: 3.3 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 3.6
Reflection shellResolution: 1.84→1.97 Å / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4482 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RXD

6rxd


Resolution: 1.84→70.569 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.93
RfactorNum. reflection% reflection
Rfree0.2388 4453 4.93 %
Rwork0.2074 --
obs0.209 90352 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.84→70.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7719 0 82 1433 9234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048113
X-RAY DIFFRACTIONf_angle_d0.68911051
X-RAY DIFFRACTIONf_dihedral_angle_d7.0946485
X-RAY DIFFRACTIONf_chiral_restr0.0421137
X-RAY DIFFRACTIONf_plane_restr0.0041457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.86090.36831210.34242915X-RAY DIFFRACTION100
1.8609-1.88280.37711530.33652791X-RAY DIFFRACTION99
1.8828-1.90580.33751390.32222901X-RAY DIFFRACTION100
1.9058-1.92990.38971240.3132839X-RAY DIFFRACTION100
1.9299-1.95530.32091460.29872854X-RAY DIFFRACTION100
1.9553-1.98210.30331430.29092832X-RAY DIFFRACTION99
1.9821-2.01040.35331590.28132842X-RAY DIFFRACTION99
2.0104-2.04040.30281500.27762822X-RAY DIFFRACTION99
2.0404-2.07230.30851670.26882839X-RAY DIFFRACTION99
2.0723-2.10630.33241310.25832855X-RAY DIFFRACTION100
2.1063-2.14260.30041620.24672841X-RAY DIFFRACTION100
2.1426-2.18160.29111280.23432874X-RAY DIFFRACTION100
2.1816-2.22350.26691270.22952880X-RAY DIFFRACTION100
2.2235-2.26890.23721330.21562890X-RAY DIFFRACTION100
2.2689-2.31820.2521350.20672854X-RAY DIFFRACTION100
2.3182-2.37220.24961380.21722874X-RAY DIFFRACTION100
2.3722-2.43150.27181310.20792874X-RAY DIFFRACTION100
2.4315-2.49730.20741660.20982852X-RAY DIFFRACTION100
2.4973-2.57070.26971440.20262873X-RAY DIFFRACTION100
2.5707-2.65370.2591780.19892840X-RAY DIFFRACTION100
2.6537-2.74860.2341580.19572848X-RAY DIFFRACTION100
2.7486-2.85860.20121610.18662859X-RAY DIFFRACTION100
2.8586-2.98870.22151520.18932863X-RAY DIFFRACTION100
2.9887-3.14630.2381410.17922911X-RAY DIFFRACTION100
3.1463-3.34340.20311520.17132845X-RAY DIFFRACTION100
3.3434-3.60160.19741440.15872888X-RAY DIFFRACTION100
3.6016-3.9640.17571380.14422905X-RAY DIFFRACTION100
3.964-4.53750.17071350.14312906X-RAY DIFFRACTION100
4.5375-5.71630.162230.15732791X-RAY DIFFRACTION100
5.7163-70.6210.2011740.19072941X-RAY DIFFRACTION100

+
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