[English] 日本語
Yorodumi
- PDB-7t5e: Neutron structure of Neurospora crassa Polysaccharide Monooxygena... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t5e
TitleNeutron structure of Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) low pH vapor exchange
ComponentsLytic polysaccharide monooxygenase
KeywordsOXIDOREDUCTASE / LPMO / monooxygenase / PMO / metalloproteins
Function / homologyAuxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61) / monooxygenase activity / hydrolase activity / extracellular region / metal ion binding / COPPER (II) ION / Lytic polysaccharide monooxygenase
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchroder, G.C. / Meilleur, F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institute of Food and Agriculture (NIFA, United States)Hatch 211001 United States
National Research Foundation in South Africa United States
Department of Energy (DOE, United States) United States
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 1.1Apr 3, 2024Group: 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: Lytic polysaccharide monooxygenase
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8986
Polymers46,5982
Non-polymers1,3004
Water6,990388
1
A: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9493
Polymers23,2991
Non-polymers6502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9493
Polymers23,2991
Non-polymers6502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.296, 42.269, 70.413
Angle α, β, γ (deg.)90.000, 98.470, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#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 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 % / Description: Crystals form rectangular shapes.
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.4 / Details: PEG 3350, HEPES

-
Data collection

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-IDSerial crystal experiment
1295Room temperature1N
2295Room temperature1N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-00711.54
SPALLATION SOURCEORNL Spallation Neutron Source MANDI22-4
Detector
TypeIDDetectorDate
DECTRIS EIGER R 4M1PIXELOct 25, 2018
ORNL ANGER CAMERA2DIFFRACTOMETERJul 17, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
221
341
Reflection

Biso Wilson estimate: 17.17 Å2 / Entry-ID: 7T5E

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRrim(I) allDiffraction-IDNet I/σ(I)
1.9-12.653095097.566.10.9910.11520.1258115.24
2.14-14.651896384.6540.970.15320.1751210.01
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
1.9-1.94.10.2994.428590.880.3443191.75
2.14-2.223.30.3283.0216550.3630.3824274.75

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
Coot0.8.9.2model building
LaueViewdata scaling
Refinement

SU ML: 0.18 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.75 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5TKH

5tkh

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)
1.9-12.662X-RAY DIFFRACTION91.1323.52753.760.1820.12750.1303155729391309485.0397.961.34
2.144-14.649NEUTRON DIFFRACTION0.21370.14440.148954187705.0884.980
Refinement stepCycle: final / Resolution: 1.9→12.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 155 1167 4593
Biso mean--47.9 33.12 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01018106
X-RAY DIFFRACTIONf_angle_d1.321813628
X-RAY DIFFRACTIONf_chiral_restr0.0707571
X-RAY DIFFRACTIONf_plane_restr0.00711339
X-RAY DIFFRACTIONf_dihedral_angle_d21.05332075
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1443-2.25690.29891620.20882254NEUTRON DIFFRACTION77
2.2569-2.39780.2791150.19442532NEUTRON DIFFRACTION85
2.3978-2.5820.26911540.17832501NEUTRON DIFFRACTION84
2.582-2.84010.22981250.1572540NEUTRON DIFFRACTION85
2.8401-3.24720.22321230.14692635NEUTRON DIFFRACTION88
3.2472-4.07640.21271390.1352669NEUTRON DIFFRACTION89
4.0764-14.6490.16641360.11742685NEUTRON DIFFRACTION87
1.9-1.96110.25541330.16472476X-RAY DIFFRACTION91
1.9611-2.03090.23361420.15852575X-RAY DIFFRACTION96
2.0309-2.11190.22151260.14782683X-RAY DIFFRACTION98
2.1119-2.20750.18881680.14232661X-RAY DIFFRACTION99
2.2075-2.32320.22241320.1462660X-RAY DIFFRACTION99
2.3232-2.46780.19911430.13892666X-RAY DIFFRACTION99
2.4678-2.65670.2111510.14152696X-RAY DIFFRACTION99
2.6567-2.92110.19831470.13712702X-RAY DIFFRACTION100
2.9211-3.3370.19341350.1322738X-RAY DIFFRACTION99
3.337-4.1790.161320.10182751X-RAY DIFFRACTION99
4.179-12.6620.12081480.10052783X-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