[English] 日本語
Yorodumi
- PDB-5wsz: Crystal structure of a lytic polysaccharide monooxygenase,BtLPMO1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wsz
TitleCrystal structure of a lytic polysaccharide monooxygenase,BtLPMO10A, from Bacillus thuringiensis
ComponentsLpmO10A
KeywordsOXIDOREDUCTASE / copper-dependent / monooxygenase / AA10
Function / homology
Function and homology information


transferase activity / metal ion binding
Similarity search - Function
chitin-binding protein cbp21 / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / LpmO10A / Acetyltransferase domain protein
Similarity search - Component
Biological speciesBacillus thuringiensis subsp. kurstaki (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.565 Å
AuthorsZhao, Y. / Zhang, H. / Yin, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31300668 China
CitationJournal: To Be Published
Title: Crystal structure of a lytic polysaccharide monooxygenase,BtLPMO10A, from Bacillus thuringiensis
Authors: Zhao, Y. / Zhang, H. / Yin, H.
History
DepositionDec 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LpmO10A
B: LpmO10A
C: LpmO10A
D: LpmO10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7458
Polymers74,4914
Non-polymers2544
Water2,342130
1
A: LpmO10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6862
Polymers18,6231
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area7280 Å2
MethodPISA
2
B: LpmO10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6862
Polymers18,6231
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area7230 Å2
MethodPISA
3
C: LpmO10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6862
Polymers18,6231
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area7140 Å2
MethodPISA
4
D: LpmO10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6862
Polymers18,6231
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.021, 73.446, 113.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
LpmO10A


Mass: 18622.801 Da / Num. of mol.: 4 / Fragment: UNP residues 35-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis subsp. kurstaki (bacteria)
Gene: lpmO10A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0C5K362, UniProt: A0A0F6FRT6*PLUS
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 20252 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.072 / Net I/σ(I): 10.9
Reflection shellResolution: 2.57→2.66 Å / Rmerge(I) obs: 0.784 / Rpim(I) all: 0.31 / % possible all: 91.06

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHENIXphasing
HKL-3000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BEM

2bem


Resolution: 2.565→47.118 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 896 4.87 %RANDOM
Rwork0.2035 ---
obs0.2058 18385 91.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.565→47.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 4 130 5378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035404
X-RAY DIFFRACTIONf_angle_d0.8417375
X-RAY DIFFRACTIONf_dihedral_angle_d12.6481923
X-RAY DIFFRACTIONf_chiral_restr0.035785
X-RAY DIFFRACTIONf_plane_restr0.006962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5649-2.72560.3801890.28092017X-RAY DIFFRACTION63
2.7256-2.9360.32871270.26872676X-RAY DIFFRACTION85
2.936-3.23140.33241640.24863109X-RAY DIFFRACTION99
3.2314-3.69890.24631580.21413178X-RAY DIFFRACTION100
3.6989-4.65950.22341890.17393186X-RAY DIFFRACTION100
4.6595-47.12550.20381690.17223323X-RAY DIFFRACTION99

+
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