[English] 日本語
Yorodumi
- PDB-7t5d: Neutron structure of Neurospora crassa Lytic Polysaccharide Monoo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t5d
TitleNeutron structure of Neurospora crassa Lytic Polysaccharide Monooxygenase 9D (NcLPMO9D) ascorbate soak
ComponentsLytic polysaccharide monooxygenase
KeywordsOXIDOREDUCTASE / LPMO / monooxygenase / PMO / metalloproteins / copper
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / extracellular region / metal ion binding
Similarity search - Function
Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61)
Similarity search - Domain/homology
COPPER (II) ION / OXYGEN MOLECULE / HYDROGEN PEROXIDE / lytic cellulose monooxygenase (C4-dehydrogenating)
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchroder, G.C. / Meilleur, F.
Funding support South Africa, 3items
OrganizationGrant numberCountry
National Institute of Food and Agriculture (NIFA, United States)Hatch 211001 South Africa
National Research Foundation in South Africa South Africa
Department of Energy (DOE, United States) South Africa
Citation
Journal: Chem Sci / Year: 2022
Title: Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase.
Authors: Schroder, G.C. / O'Dell, W.B. / Webb, S.P. / Agarwal, P.K. / Meilleur, F.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2021
Title: Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions.
Authors: Schroder, G.C. / O'Dell, W.B. / Swartz, P.D. / Meilleur, F.
History
DepositionDec 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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: Lytic polysaccharide monooxygenase
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6408
Polymers46,5982
Non-polymers1,0426
Water7,440413
1
A: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8535
Polymers23,2991
Non-polymers5544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7873
Polymers23,2991
Non-polymers4882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.730, 42.180, 69.760
Angle α, β, γ (deg.)90.000, 99.000, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Lytic polysaccharide monooxygenase / Related to cel1 protein


Mass: 23299.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: G15G9.090, GE21DRAFT_7469 / Production host: Komagataella pastoris (fungus) / Strain (production host): Superman5 / References: UniProt: Q8WZQ2
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 417 molecules

#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.3 % / Description: Crystals form rectangular shapes.
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6 / Details: PEG 3350, HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2.0-4.0
DetectorType: ORNL ANGER CAMERA / Detector: DIFFRACTOMETER / Date: Nov 15, 2018
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 2.4→14.791 Å / Num. obs: 14168 / % possible obs: 91.16 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.17 Å2 / CC1/2: 0.956 / Rmerge(I) obs: 0.1851 / Rrim(I) all: 0.2148 / Net I/σ(I): 7.15
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.2737 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 1300 / CC1/2: 0.297 / Rrim(I) all: 0.3327 / % possible all: 84.86

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Mantiddata reduction
LaueViewdata scaling
PHASERphasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TKH

5tkh


Resolution: 2.4→14.791 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 2.34 / Phase error: 31.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3088 710 5.01 %Random selection
Rwork0.2286 13457 --
obs0.2325 14167 91.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.48 Å2 / Biso mean: 38.9543 Å2 / Biso min: 21.65 Å2
Refinement stepCycle: final / Resolution: 2.4→14.79 Å
LigandSolventTotal
Num. atoms118 1242 7769
Biso mean41.55 40.48 -
Num. residues--446
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.00637494
NEUTRON DIFFRACTIONf_angle_d0.688812422
NEUTRON DIFFRACTIONf_chiral_restr0.0503524
NEUTRON DIFFRACTIONf_plane_restr0.00411258
NEUTRON DIFFRACTIONf_dihedral_angle_d17.57451799
LS refinement shell

Refine-ID: NEUTRON DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.58440.35991260.28582477260385
2.5844-2.84280.35931400.27582623276390
2.8428-3.25040.32661450.2432731287694
3.2504-4.08080.2791560.22212862301897
4.0808-14.79090.28661430.19272764290792

+
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