[English] 日本語
Yorodumi
- PDB-6xof: Crystal structure of SCLam, a non-specific endo-beta-1,3(4)-gluca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xof
TitleCrystal structure of SCLam, a non-specific endo-beta-1,3(4)-glucanase from family GH16
ComponentsGH16 family protein
KeywordsHYDROLASE / metagenomics / beta-glucan / endo-1 / 3(4)-beta-glucanases
Function / homology
Function and homology information


glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLiberato, M.V. / Bernardes, A. / Polikarpov, I. / Squina, F.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/04105-4 Brazil
Sao Paulo Research Foundation (FAPESP)2015/50590-4 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)310177/2011-1 Brazil
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Insights into the dual cleavage activity of the GH16 laminarinase enzyme class on beta-1,3 and beta-1,4 glycosidic bonds.
Authors: Liberato, M.V. / Teixeira Prates, E. / Goncalves, T.A. / Bernardes, A. / Vilela, N. / Fattori, J. / Ematsu, G.C. / Chinaglia, M. / Machi Gomes, E.R. / Migliorini Figueira, A.C. / Damasio, A. ...Authors: Liberato, M.V. / Teixeira Prates, E. / Goncalves, T.A. / Bernardes, A. / Vilela, N. / Fattori, J. / Ematsu, G.C. / Chinaglia, M. / Machi Gomes, E.R. / Migliorini Figueira, A.C. / Damasio, A. / Polikarpov, I. / Skaf, M.S. / Squina, F.M.
History
DepositionJul 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GH16 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4633
Polymers30,3311
Non-polymers1322
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.855, 46.673, 115.055
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein GH16 family protein


Mass: 30330.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Metagenomics
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: sclam / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: A0A0B5H9B3, glucan endo-1,3-beta-D-glucosidase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.1 M DL-Malic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→46.67 Å / Num. obs: 37616 / % possible obs: 99.4 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.044 / Rrim(I) all: 0.062 / Net I/σ(I): 10.6 / Num. measured all: 70423
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.531.80.398328417880.7330.3980.5631.497.2
8.22-46.671.50.0134412890.9990.0130.01924.199.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.5 Å43.25 Å
Translation1.5 Å43.25 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
APEX 2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ILN

3iln


Resolution: 1.5→43.29 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1591 / WRfactor Rwork: 0.1348 / FOM work R set: 0.8827 / SU B: 2.64 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0716 / SU Rfree: 0.0698 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 1815 4.8 %RANDOM
Rwork0.1452 ---
obs0.1463 35738 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.75 Å2 / Biso mean: 9.543 Å2 / Biso min: 2.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0 Å2
2---0.16 Å20 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.5→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 19 468 2587
Biso mean--5 23.43 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132229
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181988
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.6453038
X-RAY DIFFRACTIONr_angle_other_deg1.551.5834592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7775280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16322.857119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53515347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1021511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 125 -
Rwork0.261 2555 -
all-2680 -
obs--97.07 %
Refinement TLS params.Method: refined / Origin x: 5.1013 Å / Origin y: 3.6928 Å / Origin z: 15.216 Å
111213212223313233
T0.0068 Å20.0027 Å20.0007 Å2-0.0024 Å20.0008 Å2--0.0096 Å2
L0.0733 °20.0981 °2-0.0341 °2-0.1477 °2-0.0596 °2--0.1774 °2
S0.0015 Å °-0.003 Å °-0.0001 Å °0.0034 Å °-0.0042 Å °0.0115 Å °0.0065 Å °0.0174 Å °0.0027 Å °

+
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