[English] 日本語
Yorodumi
- PDB-5b0p: Beta-1,2-Mannobiose phosphorylase from Listeria innocua - glycero... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b0p
TitleBeta-1,2-Mannobiose phosphorylase from Listeria innocua - glycerol complex
ComponentsLin0857 protein
KeywordsTRANSFERASE / Glycoside phosphorylase
Function / homologybeta-1,2-mannobiose phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / glycosyltransferase activity / Beta-1,2-mannobiose phosphorylase
Function and homology information
Biological speciesListeria innocua Clip11262 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTsuda, T. / Arakawa, T. / Fushinobu, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
The Ministry of Agriculture, Forestry and Fisheries, Japan25010A Japan
CitationJournal: Febs Lett. / Year: 2015
Title: Characterization and crystal structure determination of beta-1,2-mannobiose phosphorylase from Listeria innocua
Authors: Tsuda, T. / Nihira, T. / Chiku, K. / Suzuki, E. / Arakawa, T. / Nishimoto, M. / Kitaoka, M. / Nakai, H. / Fushinobu, S.
History
DepositionNov 2, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lin0857 protein
B: Lin0857 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,04217
Polymers82,2202
Non-polymers1,82215
Water12,629701
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-15 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.559, 146.559, 106.324
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Lin0857 protein / beta-1 / 2-Mannobiose phosphorylase


Mass: 41110.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua Clip11262 (bacteria) / Strain: CLIP 11262 / Gene: lin0857 / Plasmid: pET24a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3)-RIL / References: UniProt: Q92DF6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 1.8 M (NH4)2SO4, 10 mM CoCl2, 0.1 M MES-NaOH

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 27, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 103595 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 50.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 5.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VKD

1vkd


Resolution: 1.9→34.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.295 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19698 5168 5 %RANDOM
Rwork0.16458 ---
obs0.16622 98246 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.598 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.095 Å
Refinement stepCycle: 1 / Resolution: 1.9→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5640 0 107 701 6448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0195872
X-RAY DIFFRACTIONr_bond_other_d0.0020.025461
X-RAY DIFFRACTIONr_angle_refined_deg2.2051.9827957
X-RAY DIFFRACTIONr_angle_other_deg1.112312615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2055707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59824.514288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02615958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2751530
X-RAY DIFFRACTIONr_chiral_restr0.1660.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0216579
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021319
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_it3.022.7492834
X-RAY DIFFRACTIONr_mcbond_other3.0172.7482833
X-RAY DIFFRACTIONr_mcangle_it3.5484.1093539
X-RAY DIFFRACTIONr_mcangle_other3.5484.1113540
X-RAY DIFFRACTIONr_scbond_it4.2283.173038
X-RAY DIFFRACTIONr_scbond_other4.2283.173038
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8784.5914419
X-RAY DIFFRACTIONr_long_range_B_refined7.3623.7846921
X-RAY DIFFRACTIONr_long_range_B_other7.3623.7856922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 362 -
Rwork0.221 7173 -
obs--99.88 %

+
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