[English] 日本語
Yorodumi
- PDB-7pu1: High resolution X-ray structure of Thermoascus aurantiacus LPMO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pu1
TitleHigh resolution X-ray structure of Thermoascus aurantiacus LPMO
ComponentsGh61 isozyme a
KeywordsOXIDOREDUCTASE / Copper binding protein / Beta-sandwich fold / Auxillary
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulase activity / 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 / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsBanerjee, S. / Frandsen, K.E.H. / Singh, R.K. / Bjerrum, M.J. / Lo Leggio, L.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Sweden
Danish Council for Independent Research8021-00273B Sweden
Swedish Research Council2018-04969; 2019-02496 Sweden
CitationJournal: Biomolecules / Year: 2022
Title: Protonation State of an Important Histidine from High Resolution Structures of Lytic Polysaccharide Monooxygenases.
Authors: Banerjee, S. / Muderspach, S.J. / Tandrup, T. / Frandsen, K.E.H. / Singh, R.K. / Ipsen, J.O. / Hernandez-Rollan, C. / Norholm, M.H.H. / Bjerrum, M.J. / Johansen, K.S. / Lo Leggio, L.
History
DepositionSep 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Gh61 isozyme a
BBB: Gh61 isozyme a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,07925
Polymers48,8362
Non-polymers1,24323
Water12,701705
1
AAA: Gh61 isozyme a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,02212
Polymers24,4181
Non-polymers60411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Gh61 isozyme a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,05713
Polymers24,4181
Non-polymers63912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.653, 89.046, 70.470
Angle α, β, γ (deg.)90.000, 103.335, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

-
Components

#1: Protein Gh61 isozyme a


Mass: 24418.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: G3XAP7, cellulase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 20m M MgCl2 and 22 %(w/v) polyacrylic acid 5100 sodium salt

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9538 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9538 Å / Relative weight: 1
ReflectionResolution: 1.06→37.34 Å / Num. obs: 171807 / % possible obs: 84.2 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rrim(I) all: 0.054 / Net I/σ(I): 18.57
Reflection shellResolution: 1.06→1.1 Å / Mean I/σ(I) obs: 3.6 / Num. unique obs: 12524 / CC1/2: 0.89 / Rrim(I) all: 0.44

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
TRUNCATEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YET

2yet


Resolution: 1.06→37.37 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / WRfactor Rfree: 0.144 / WRfactor Rwork: 0.118 / SU B: 0.651 / SU ML: 0.014 / Average fsc free: 0.9715 / Average fsc work: 0.9751 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.026
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.11851 8758 5.097 %
Rwork0.11735 163069 -
all0.119 --
obs-163069 84.244 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.983 Å2
Baniso -1Baniso -2Baniso -3
1-0.072 Å20 Å20.194 Å2
2---0.221 Å2-0 Å2
3---0.052 Å2
Refinement stepCycle: LAST / Resolution: 1.06→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 49 719 4213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0133731
X-RAY DIFFRACTIONr_bond_other_d0.0070.0173256
X-RAY DIFFRACTIONr_angle_refined_deg2.3041.6575188
X-RAY DIFFRACTIONr_angle_other_deg1.6241.5717658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.1325.423520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.73125.605157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88615494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.868153
X-RAY DIFFRACTIONr_chiral_restr0.1290.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025153
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02699
X-RAY DIFFRACTIONr_nbd_refined0.2530.2709
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.23236
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21848
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.10.21675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2451
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.27
X-RAY DIFFRACTIONr_nbd_other0.1030.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.259
X-RAY DIFFRACTIONr_mcbond_it1.3761.1361873
X-RAY DIFFRACTIONr_mcbond_other1.3561.1331871
X-RAY DIFFRACTIONr_mcangle_it1.8341.7172351
X-RAY DIFFRACTIONr_mcangle_other1.821.7162351
X-RAY DIFFRACTIONr_scbond_it3.6251.3291858
X-RAY DIFFRACTIONr_scbond_other3.6241.3291859
X-RAY DIFFRACTIONr_scangle_it3.241.9182814
X-RAY DIFFRACTIONr_scangle_other3.241.9192815
X-RAY DIFFRACTIONr_lrange_it3.71516.284399
X-RAY DIFFRACTIONr_lrange_other3.27114.9494165
X-RAY DIFFRACTIONr_rigid_bond_restr8.90636987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.0880.3022270.274658X-RAY DIFFRACTION32.4563
1.088-1.1170.1893620.1686568X-RAY DIFFRACTION47.2973
1.117-1.150.1694010.1458183X-RAY DIFFRACTION60.0784
1.15-1.1850.1514840.1279895X-RAY DIFFRACTION75.0959
1.185-1.2240.1526540.12211888X-RAY DIFFRACTION93.1936
1.224-1.2670.1236230.10411680X-RAY DIFFRACTION94.6603
1.267-1.3150.1336250.10711293X-RAY DIFFRACTION95.0929
1.315-1.3680.1236350.08710928X-RAY DIFFRACTION95.6489
1.368-1.4290.1215980.08210513X-RAY DIFFRACTION95.9416
1.429-1.4990.1115630.08110168X-RAY DIFFRACTION96.606
1.499-1.580.1135080.0789699X-RAY DIFFRACTION96.9878
1.58-1.6760.1134980.089195X-RAY DIFFRACTION97.2509
1.676-1.7910.1254340.098754X-RAY DIFFRACTION97.7759
1.791-1.9350.1214070.1068101X-RAY DIFFRACTION97.7594
1.935-2.1190.1344160.1147514X-RAY DIFFRACTION98.4971
2.119-2.3690.1313510.1186827X-RAY DIFFRACTION98.5718
2.369-2.7350.1443450.1276015X-RAY DIFFRACTION99.0809
2.735-3.3480.1562930.1365108X-RAY DIFFRACTION99.2284
3.348-4.730.1552160.1363956X-RAY DIFFRACTION98.6055
4.73-37.370.1991180.192126X-RAY DIFFRACTION95.0445

+
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