[English] 日本語
Yorodumi
- PDB-6kcv: Structure of alginate lyase Aly36B mutant K143A/Y185A in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kcv
TitleStructure of alginate lyase Aly36B mutant K143A/Y185A in complex with alginate tetrasaccharide
ComponentsAlginate lyase
KeywordsLYASE / Alginate lyase
Function / homology: / Polysaccharide lyase 14 / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesChitinophaga sp. MD30 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.282 Å
AuthorsDong, F. / Zhang, Y.Z. / Chen, X.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31870052 China
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Alginate Lyase Aly36B is a New Bacterial Member of the Polysaccharide Lyase Family 36 and Catalyzes by a Novel Mechanism With Lysine as Both the Catalytic Base and Catalytic Acid.
Authors: Dong, F. / Xu, F. / Chen, X.L. / Li, P.Y. / Li, C.Y. / Li, F.C. / Chen, Y. / Wang, P. / Zhang, Y.Z.
History
DepositionJun 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Alginate lyase
A: Alginate lyase
C: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7979
Polymers80,5093
Non-polymers2,2886
Water10,683593
1
B: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5993
Polymers26,8361
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-3 kcal/mol
Surface area9410 Å2
MethodPISA
2
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5993
Polymers26,8361
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-6 kcal/mol
Surface area9470 Å2
MethodPISA
3
C: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5993
Polymers26,8361
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-6 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.580, 187.526, 91.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

21A-565-

HOH

-
Components

#1: Protein Alginate lyase


Mass: 26836.303 Da / Num. of mol.: 3 / Mutation: K109A, Y151A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinophaga sp. MD30 (bacteria) / Gene: CK934_20815 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A249T061
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 722.510 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122A-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: potassium phosphate dibasic, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.282→93.77 Å / Num. obs: 41253 / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.37
Reflection shellResolution: 2.282→2.38 Å / Rmerge(I) obs: 0.12 / Num. unique obs: 4053

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.282→35.342 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 2087 5.07 %
Rwork0.1598 39037 -
obs0.1621 41124 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.3 Å2 / Biso mean: 29.4081 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: final / Resolution: 2.282→35.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5694 0 150 593 6437
Biso mean--35.94 34.11 -
Num. residues----732
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.282-2.3350.27891250.1755211382
2.335-2.39340.21431490.16552612100
2.3934-2.45810.20791190.17132615100
2.4581-2.53040.22671140.16892628100
2.5304-2.6120.23191700.16612592100
2.612-2.70540.23221510.17012616100
2.7054-2.81360.23791490.17382592100
2.8136-2.94160.23591340.17272643100
2.9416-3.09660.25331500.17382601100
3.0966-3.29050.21491450.17022648100
3.2905-3.54440.19341450.16112646100
3.5444-3.90060.17061450.15182625100
3.9006-4.46410.16431180.13012684100
4.4641-5.62070.16711160.13142720100
5.6207-35.3420.21431570.1885270297

+
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://pdbjlvh1.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