[English] 日本語
Yorodumi
- PDB-9qyv: MINPP1 from Bacteroides thetaiotaomicron Q276W mutant complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qyv
TitleMINPP1 from Bacteroides thetaiotaomicron Q276W mutant complex with myo-inositol hexakissulfate
ComponentsMultiple inositol polyphosphate phosphatase 1
KeywordsHYDROLASE / Histidine phosphatase / phytase / mutant / complex
Function / homology
Function and homology information


multiple inositol-polyphosphate phosphatase / 2,3-bisphosphoglycerate 3-phosphatase / hydrolase activity / 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 speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShang, X.Y. / Salmon, M. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M022978/1 United Kingdom
CitationJournal: To Be Published
Title: A Structural Basis for the Stereospecificity of Multiple Inositol Polyphosphate Phosphatases
Authors: Salmon, M. / Shang, X.Y. / Li, A.W.H. / Hemmings, A.M.
History
DepositionApr 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multiple inositol polyphosphate phosphatase 1
B: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6006
Polymers98,5232
Non-polymers2,0774
Water8,233457
1
A: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9222
Polymers49,2621
Non-polymers6611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple inositol polyphosphate phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6784
Polymers49,2621
Non-polymers1,4163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.311, 120.823, 75.719
Angle α, β, γ (deg.)90.000, 107.630, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Multiple inositol polyphosphate phosphatase 1 / 2 / 3-bisphosphoglycerate 3-phosphatase


Mass: 49261.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_4744 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q89YI8, multiple inositol-polyphosphate phosphatase, 2,3-bisphosphoglycerate 3-phosphatase
#2: Chemical ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O24S6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2 M ammonium acetate pH 5.0 18 % (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→48.45 Å / Num. obs: 69085 / % possible obs: 98.06 % / Redundancy: 7.1 % / Biso Wilson estimate: 26.39 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.37
Reflection shellResolution: 1.9→1.968 Å / Mean I/σ(I) obs: 2.46 / Num. unique obs: 6544 / CC1/2: 0.883

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.45 Å / SU ML: 0.1581 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.2982
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2085 3432 4.97 %
Rwork0.1702 65653 -
obs0.1721 69085 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6496 0 113 457 7066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826867
X-RAY DIFFRACTIONf_angle_d1.06839349
X-RAY DIFFRACTIONf_chiral_restr0.05971018
X-RAY DIFFRACTIONf_plane_restr0.00871163
X-RAY DIFFRACTIONf_dihedral_angle_d10.0967957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.22521210.21952444X-RAY DIFFRACTION91.97
1.93-1.950.29351230.20712511X-RAY DIFFRACTION93.97
1.95-1.980.25031320.19812570X-RAY DIFFRACTION96.16
1.98-2.010.24811340.182614X-RAY DIFFRACTION97.38
2.01-2.050.20961440.1762586X-RAY DIFFRACTION97.22
2.05-2.080.24291620.17622594X-RAY DIFFRACTION98.04
2.08-2.120.23361420.17592591X-RAY DIFFRACTION97.92
2.12-2.160.21621390.17222646X-RAY DIFFRACTION97.58
2.16-2.20.22081510.16142554X-RAY DIFFRACTION98.36
2.2-2.250.21981360.1662646X-RAY DIFFRACTION98.37
2.25-2.30.24611330.17142634X-RAY DIFFRACTION97.84
2.3-2.360.21581460.16252649X-RAY DIFFRACTION97.97
2.36-2.430.1941430.16992611X-RAY DIFFRACTION98.6
2.43-2.50.17521240.17132656X-RAY DIFFRACTION98.72
2.5-2.580.23031340.17242626X-RAY DIFFRACTION98.71
2.58-2.670.22531400.17042634X-RAY DIFFRACTION98.65
2.67-2.780.2241510.17142639X-RAY DIFFRACTION98.59
2.78-2.90.22951610.17162645X-RAY DIFFRACTION99.01
2.9-3.060.20791160.16812662X-RAY DIFFRACTION99.29
3.06-3.250.18781200.17162689X-RAY DIFFRACTION98.84
3.25-3.50.16551520.17292644X-RAY DIFFRACTION99.61
3.5-3.850.22841480.15832660X-RAY DIFFRACTION99.33
3.85-4.410.18981180.16482706X-RAY DIFFRACTION99.44
4.41-5.550.16971210.16042714X-RAY DIFFRACTION99.68
5.55-48.450.2251410.17882728X-RAY DIFFRACTION99.48
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9269471660620.1521401096330.0961427422691.2118564058-0.2584972365611.239891479450.0385323833299-0.0946752853848-0.06533060863520.0163104778427-0.01435194732870.0828963443639-0.0145293789412-0.0790551660936-0.01454796847620.1363517775810.0200599933927-0.002226827780290.1753200291260.004041150684410.14031865994316.4135895315-8.796662627470.805304442228
21.09380722422-0.209709348043-0.02477161430920.9496533762280.2301706614361.04006540813-0.01019781861190.06748237414760.04949151257160.0146295825831-0.03028609227910.0547664111021-0.08612943198180.001454693304040.03893759590150.171209913771-0.0268831281916-0.007846431470990.1661847776260.008476755565360.14896543402425.722557178311.099544965531.9922485115
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 21 through 424)AA21 - 4241 - 397
22(chain 'B' and resid 20 through 424)BB20 - 4241 - 398

+
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