[English] 日本語
Yorodumi
- PDB-7v6i: Crystal structure of lacto-N-biosidase BsaX from Bifidobacterium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v6i
TitleCrystal structure of lacto-N-biosidase BsaX from Bifidobacterium saguini, lacto-N-biose complex
ComponentsLacto-N-biosidase
KeywordsHYDROLASE / Glycoside hydrolase / lacto-N-biosidase / lacto-N-biose complex
Function / homology
Function and homology information


carbohydrate metabolic process / membrane
Similarity search - Function
Long Rib domain / Long Rib domain / FIVAR domain / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / Immunoglobulin-like fold
Similarity search - Domain/homology
Long Rib domain-containing protein
Similarity search - Component
Biological speciesBifidobacterium saguini DSM 23967 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsYamada, C. / Fushinobu, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16J09251 Japan
Japan Society for the Promotion of Science (JSPS)18K14388 Japan
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2022
Title: Crystal structures of glycoside hydrolase family 136 lacto-N-biosidases from monkey gut- and human adult gut bacteria.
Authors: Yamada, C. / Katayama, T. / Fushinobu, S.
History
DepositionAug 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: 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: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4372
Polymers68,0531
Non-polymers3831
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint7 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.240, 113.240, 79.097
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Lacto-N-biosidase


Mass: 68053.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium saguini DSM 23967 (bacteria)
Gene: BISA_2023 / Plasmid: pET23b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A087D8U9
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.5M ammonium sulfate, 0.1M sodium acetate (pH 4.6), 30% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 22, 2018
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→49.08 Å / Num. obs: 20374 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 15.86 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.061 / Rrim(I) all: 0.194 / Net I/σ(I): 11.2
Reflection shellResolution: 2.51→2.61 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2262 / CC1/2: 0.913 / Rpim(I) all: 0.228 / Rrim(I) all: 0.732 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GQF

5gqf


Resolution: 2.51→49.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.99 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 1.391 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22759 972 4.8 %RANDOM
Rwork0.15664 ---
obs0.15995 19380 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.598 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.33 Å20 Å2
2--0.65 Å2-0 Å2
3----2.12 Å2
Refinement stepCycle: 1 / Resolution: 2.51→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 26 104 4747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134750
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184129
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6466485
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5969497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8725596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89224.312269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28715693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5261519
X-RAY DIFFRACTIONr_chiral_restr0.0650.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021133
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_it1.7862.6472387
X-RAY DIFFRACTIONr_mcbond_other1.7852.6462386
X-RAY DIFFRACTIONr_mcangle_it2.6863.9682982
X-RAY DIFFRACTIONr_mcangle_other2.6863.9692983
X-RAY DIFFRACTIONr_scbond_it2.2352.8842362
X-RAY DIFFRACTIONr_scbond_other2.2282.8842362
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5024.2483503
X-RAY DIFFRACTIONr_long_range_B_refined4.81930.9865309
X-RAY DIFFRACTIONr_long_range_B_other4.82130.9855309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 71 -
Rwork0.186 1400 -
obs--100 %

+
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