[English] 日本語
Yorodumi
- PDB-8hhv: endo-alpha-D-arabinanase EndoMA1 from Microbacterium arabinogalac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hhv
Titleendo-alpha-D-arabinanase EndoMA1 from Microbacterium arabinogalactanolyticum
Componentsendo-alpha-D-arabinanase
KeywordsHYDROLASE / D-arabinan / anomer-retaining glycoside hydrolase
Function / homologyGalactose-binding domain-like / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesMicrobacterium arabinogalactanolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsNakashima, C. / Li, J. / Arakawa, T. / Yamada, C. / Ishiwata, A. / Fujita, K. / Fushinobu, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H00929 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Identification and characterization of endo-alpha-, exo-alpha-, and exo-beta-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria.
Authors: Shimokawa, M. / Ishiwata, A. / Kashima, T. / Nakashima, C. / Li, J. / Fukushima, R. / Sawai, N. / Nakamori, M. / Tanaka, Y. / Kudo, A. / Morikami, S. / Iwanaga, N. / Akai, G. / Shimizu, N. / ...Authors: Shimokawa, M. / Ishiwata, A. / Kashima, T. / Nakashima, C. / Li, J. / Fukushima, R. / Sawai, N. / Nakamori, M. / Tanaka, Y. / Kudo, A. / Morikami, S. / Iwanaga, N. / Akai, G. / Shimizu, N. / Arakawa, T. / Yamada, C. / Kitahara, K. / Tanaka, K. / Ito, Y. / Fushinobu, S. / Fujita, K.
History
DepositionNov 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: endo-alpha-D-arabinanase
B: endo-alpha-D-arabinanase
C: endo-alpha-D-arabinanase
D: endo-alpha-D-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,74332
Polymers214,9254
Non-polymers1,81828
Water31,7061760
1
A: endo-alpha-D-arabinanase
D: endo-alpha-D-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,55618
Polymers107,4632
Non-polymers1,09316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-61 kcal/mol
Surface area33240 Å2
MethodPISA
2
B: endo-alpha-D-arabinanase
hetero molecules

C: endo-alpha-D-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,18714
Polymers107,4632
Non-polymers72512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4560 Å2
ΔGint-59 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.285, 128.296, 104.019
Angle α, β, γ (deg.)90.00, 109.38, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
endo-alpha-D-arabinanase


Mass: 53731.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium arabinogalactanolyticum (bacteria)
Strain: JCM 9171 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus(DE3)-RIL
References: Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1760 / 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: 2.38 Å3/Da / Density % sol: 48.42 % / Description: Pillar/thick plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 23% PEG 3350, 0.4 M sodium thiocyanate

-
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: Dec 4, 2017
RadiationMonochromator: Numerical link type Si(111) double crysta / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→46.13 Å / Num. obs: 261209 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 11.88 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.041 / Net I/σ(I): 9.9
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 12725 / CC1/2: 0.844 / Rpim(I) all: 0.356 / % possible all: 98

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSJan 10, 2022data reduction
XDSJan 10, 2022data scaling
PHENIX1.12-2829phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→46.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.196 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21121 12950 5 %RANDOM
Rwork0.17696 ---
obs0.17867 248219 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.379 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0 Å20.27 Å2
2--1.58 Å20 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.6→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14836 0 108 1760 16704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01115366
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613201
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.64120929
X-RAY DIFFRACTIONr_angle_other_deg0.6851.56230732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.77951916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.8925104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.231102223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.22166
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217970
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023334
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_it2.0931.8257664
X-RAY DIFFRACTIONr_mcbond_other2.0911.8257664
X-RAY DIFFRACTIONr_mcangle_it2.6322.739574
X-RAY DIFFRACTIONr_mcangle_other2.6332.739575
X-RAY DIFFRACTIONr_scbond_it2.5891.9927702
X-RAY DIFFRACTIONr_scbond_other2.5891.9937703
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5182.9111354
X-RAY DIFFRACTIONr_long_range_B_refined4.61725.20817639
X-RAY DIFFRACTIONr_long_range_B_other4.61725.20917640
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 946 -
Rwork0.279 18065 -
obs--97.91 %

+
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