[English] 日本語
Yorodumi
- PDB-5iju: Structure of an AA10 Lytic Polysaccharide Monooxygenase from Baci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iju
TitleStructure of an AA10 Lytic Polysaccharide Monooxygenase from Bacillus amyloliquefaciens with Cu(II) bound
ComponentsBaAA10 Lytic Polysaccharide Monooxygenase
KeywordsOXIDOREDUCTASE / lytic polysaccharide monooxygenase / copper II / CAZy AA10
Function / homologychitin-binding protein cbp21 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta / COPPER (II) ION / :
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsGregory, R.C. / Hemsworth, G.R. / Turkenburg, J.P. / Hart, S.J. / Walton, P.H. / Davies, G.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I014802/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L000423 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L021633/1 United Kingdom
Citation
Journal: Dalton Trans / Year: 2016
Title: Activity, stability and 3-D structure of the Cu(ii) form of a chitin-active lytic polysaccharide monooxygenase from Bacillus amyloliquefaciens.
Authors: Gregory, R.C. / Hemsworth, G.R. / Turkenburg, J.P. / Hart, S.J. / Walton, P.H. / Davies, G.J.
#1: Journal: J. Am. Chem. Soc. / Year: 2013
Title: The copper active site of CBM33 polysaccharide oxygenases.
Authors: Hemsworth, G.R. / Taylor, E.J. / Kim, R.Q. / Gregory, R.C. / Lewis, S.J. / Turkenburg, J.P. / Parkin, A. / Davies, G.J. / Walton, P.H.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
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 / _pdbx_audit_support.funding_organization
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BaAA10 Lytic Polysaccharide Monooxygenase
B: BaAA10 Lytic Polysaccharide Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9857
Polymers39,6942
Non-polymers2915
Water5,080282
1
A: BaAA10 Lytic Polysaccharide Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9733
Polymers19,8471
Non-polymers1262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BaAA10 Lytic Polysaccharide Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0134
Polymers19,8471
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.779, 73.482, 75.457
Angle α, β, γ (deg.)90.000, 100.400, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

-
Components

#1: Protein BaAA10 Lytic Polysaccharide Monooxygenase / RBAM17540


Mass: 19847.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein was produced as a SUMO fusion, the SUMO domain removed using SUMO protease during purification
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: RBAM17540, BAMF_1859 / Plasmid: Champion-pETSUMO / Details (production host): Invitrogen / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: E1UUV3
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M NaOAc pH 5.0, 20 % PEG-6000, 0.2 M CaCl2 Micro seeded using crystals grown in 0.1 M MMT pH 4.0, 25 % PEG-1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→37.11 Å / Num. obs: 41043 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 7.2 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.142 / Net I/σ(I): 5.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.3 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2YOX

2yox


Resolution: 1.7→37.11 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.829 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 2062 5 %RANDOM
Rwork0.2229 ---
obs0.2249 41020 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 34.94 Å2 / Biso mean: 9.4268 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.42 Å2
2--0.28 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 11 282 3075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192876
X-RAY DIFFRACTIONr_bond_other_d00.022596
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9023912
X-RAY DIFFRACTIONr_angle_other_deg3.76635976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9795354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39724.559136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35815424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.785158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213316
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02708
X-RAY DIFFRACTIONr_mcbond_it0.6640.8451422
X-RAY DIFFRACTIONr_mcbond_other0.6640.8441421
X-RAY DIFFRACTIONr_mcangle_it1.1181.2641774
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 150 -
Rwork0.282 2892 -
all-3042 -
obs--99.25 %

+
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