[English] 日本語
Yorodumi
- PDB-6xqm: Crystal structure of SCLam E144S mutant, a non-specific endo-beta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xqm
TitleCrystal structure of SCLam E144S mutant, a non-specific endo-beta-1,3(4)-glucanase from family GH16, co-crystallized with laminarihexaose, presenting a laminaribiose and a glucose at active site
ComponentsGH16 family protein
KeywordsHYDROLASE / glycoside hydrolase / transglycosylation / endo-1 / 3(4)-beta-glucanases / metagenome
Function / homology
Function and homology information


glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
alpha-D-glucopyranose / PHOSPHATE ION / GH16 family protein
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsLiberato, M.V. / 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 9, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GH16 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9465
Polymers30,2891
Non-polymers6584
Water5,206289
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)40.170, 75.610, 83.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein GH16 family protein


Mass: 30288.746 Da / Num. of mol.: 1 / Mutation: E144S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: sclam / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0B5H9B3, glucan endo-1,3-beta-D-glucosidase

-
Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 291 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 27.5 % PEG4000, 0.2 M magnesium chloride, and 0.1 M MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.85→41.74 Å / Num. obs: 22433 / % possible obs: 99.9 % / Redundancy: 11.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.052 / Rrim(I) all: 0.179 / Net I/σ(I): 8.1 / Num. measured all: 255230 / Scaling rejects: 11353
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
1.85-1.899.61.361302613570.7810.4531.4371.399.4
9.06-41.749.50.05523122430.9990.0180.05819.399.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.11 Å36.2 Å
Translation6.11 Å36.2 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASER2.5.7phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XOF

6xof


Resolution: 1.85→36.22 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.94 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1491 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 1061 4.7 %RANDOM
Rwork0.1738 ---
obs0.1759 21312 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.78 Å2 / Biso mean: 24.389 Å2 / Biso min: 13 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2---0.44 Å20 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 1.85→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 41 289 2396
Biso mean--23.93 38.05 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132200
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171867
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.6683006
X-RAY DIFFRACTIONr_angle_other_deg1.5091.5974341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9295287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80422.605119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65815.091328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0291512
X-RAY DIFFRACTIONr_chiral_restr0.1260.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 71 -
Rwork0.327 1548 -
all-1619 -
obs--99.2 %
Refinement TLS params.Method: refined / Origin x: 14.394 Å / Origin y: -0.813 Å / Origin z: 92.159 Å
111213212223313233
T0.0821 Å2-0.0148 Å2-0.0132 Å2-0.007 Å2-0.0147 Å2--0.106 Å2
L1.2055 °2-0.0373 °2-0.0364 °2-1.7694 °2-0.7912 °2--2.7144 °2
S-0.066 Å °0.0417 Å °-0.0719 Å °0.046 Å °0.0471 Å °-0.1041 Å °-0.1037 Å °0.0242 Å °0.0188 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 266
2X-RAY DIFFRACTION1A301 - 305
3X-RAY DIFFRACTION1A401 - 689

+
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