[English] 日本語
Yorodumi
- PDB-7qqi: Sucrose phosphorylase from Faecalibaculum rodentium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qqi
TitleSucrose phosphorylase from Faecalibaculum rodentium
ComponentsAamy domain-containing protein
KeywordsTRANSFERASE / sucrose phosphorylase
Function / homology
Function and homology information


: / 1,4-alpha-oligoglucan phosphorylase activity
Similarity search - Function
Sucrose/Glucosylglycerate phosphorylase-related / Sucrose phosphorylase / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Aamy domain-containing protein
Similarity search - Component
Biological speciesFaecalibaculum rodentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsUbiparip, Z. / Capra, N. / Rozeboom, H.J. / Desmet, T. / Thunnissen, A.M.W.H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission761030European Union
CitationJournal: To Be Published
Title: Sucrose phosphorylase from Faecalibaculum rodentium
Authors: Ubiparip, Z. / Capra, N. / Rozeboom, H.J. / Thunnissen, A.M.W.H. / Desmet, T.
History
DepositionJan 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aamy domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0212
Polymers56,8991
Non-polymers1221
Water8,071448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.798, 94.409, 104.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Aamy domain-containing protein


Mass: 56898.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibaculum rodentium (bacteria) / Gene: AALO17_25870 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140DYJ4
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein was concentrated to 30 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 1 ...Details: Protein was concentrated to 30 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 1 M Na citrate, 0.1 M Tris, pH 7.0, 0.2 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.36→46 Å / Num. obs: 95834 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.056 / Rrim(I) all: 0.095 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.45-45.814.50.0266600.9990.0190.032
1.36-1.3851.2746760.450.9331.583

-
Processing

Software
NameVersionClassification
XDSdata scaling
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S9V

6s9v


Resolution: 1.36→46 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.355 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1853 4844 5.059 %
Rwork0.1495 90904 -
all0.151 --
obs-95748 99.564 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.554 Å2
Baniso -1Baniso -2Baniso -3
1--0.567 Å20 Å20 Å2
2---1.915 Å20 Å2
3---2.483 Å2
Refinement stepCycle: LAST / Resolution: 1.36→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3918 0 8 448 4374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134064
X-RAY DIFFRACTIONr_bond_other_d0.0020.0153719
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.6445513
X-RAY DIFFRACTIONr_angle_other_deg1.4211.5868563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5565486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47221.847249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73915678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9231533
X-RAY DIFFRACTIONr_chiral_restr0.0720.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02992
X-RAY DIFFRACTIONr_nbd_refined0.210.2792
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.23603
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21979
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2360
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0790.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.27
X-RAY DIFFRACTIONr_nbd_other0.170.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.222
X-RAY DIFFRACTIONr_mcbond_it1.3721.5071939
X-RAY DIFFRACTIONr_mcbond_other1.3571.5061937
X-RAY DIFFRACTIONr_mcangle_it1.7112.2762426
X-RAY DIFFRACTIONr_mcangle_other1.7142.2782427
X-RAY DIFFRACTIONr_scbond_it2.0361.7942125
X-RAY DIFFRACTIONr_scbond_other2.0351.7942126
X-RAY DIFFRACTIONr_scangle_it2.462.5923087
X-RAY DIFFRACTIONr_scangle_other2.462.5923088
X-RAY DIFFRACTIONr_lrange_it3.06218.9414797
X-RAY DIFFRACTIONr_lrange_other2.80518.4944711
X-RAY DIFFRACTIONr_rigid_bond_restr7.31737783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.3950.3033680.2826652X-RAY DIFFRACTION99.8862
1.395-1.4340.2923400.2616473X-RAY DIFFRACTION99.8534
1.434-1.4750.2883470.2456265X-RAY DIFFRACTION99.3688
1.475-1.5210.2183430.2076062X-RAY DIFFRACTION98.3267
1.521-1.570.2253070.1875945X-RAY DIFFRACTION99.9361
1.57-1.6250.2193040.1735798X-RAY DIFFRACTION99.9672
1.625-1.6870.2033110.1495569X-RAY DIFFRACTION99.915
1.687-1.7560.2192940.1455377X-RAY DIFFRACTION99.9647
1.756-1.8340.1982590.1425176X-RAY DIFFRACTION99.9081
1.834-1.9230.1682680.1354916X-RAY DIFFRACTION99.9422
1.923-2.0270.1922310.1314740X-RAY DIFFRACTION99.8193
2.027-2.150.1712460.1234439X-RAY DIFFRACTION99.3427
2.15-2.2980.1661980.1214206X-RAY DIFFRACTION99.7734
2.298-2.4830.1632180.123942X-RAY DIFFRACTION99.7841
2.483-2.7190.1721780.1353594X-RAY DIFFRACTION99.3416
2.719-3.040.1751770.1473285X-RAY DIFFRACTION99.1693
3.04-3.510.1741710.1472883X-RAY DIFFRACTION98.899
3.51-4.2970.1371280.122476X-RAY DIFFRACTION98.9362
4.297-6.0720.151980.1461966X-RAY DIFFRACTION98.9928
6.072-460.211580.1751140X-RAY DIFFRACTION97.3193

+
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