[English] 日本語
Yorodumi
- PDB-7aa2: Chaetomium thermophilum FAD-dependent oxidoreductase in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7aa2
TitleChaetomium thermophilum FAD-dependent oxidoreductase in complex with ABTS
ComponentsFAD-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Chaetomium thermophilum / glucose-methanol-choline oxidoreductase / ABTS / co-crystallization
Function / homologyChem-EBS / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / FORMIC ACID
Function and homology information
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSvecova, L. / Skalova, T. / Kolenko, P. / Koval, T. / Oestergaard, L.H. / Dohnalek, J.
Funding support Czech Republic, 6items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0109 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015043 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLQ1604 Czech Republic
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum.
Authors: Svecova, L. / Ostergaard, L.H. / Skalova, T. / Schnorr, K.M. / Koval', T. / Kolenko, P. / Stransky, J. / Sedlak, D. / Duskova, J. / Trundova, M. / Hasek, J. / Dohnalek, J.
History
DepositionSep 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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: FAD-dependent oxidoreductase
B: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,17923
Polymers128,5342
Non-polymers5,64421
Water29,7791653
1
A: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,23013
Polymers64,2671
Non-polymers2,96312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,94910
Polymers64,2671
Non-polymers2,6829
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.589, 109.799, 115.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein FAD-dependent oxidoreductase


Mass: 64267.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The provided sequence corresponds to the mass spectrometry analysis of sample used for crystallization
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / Gene: CTHT_0048040 / Production host: Aspergillus oryzae (mold)

-
Sugars , 2 types, 11 molecules

#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
#4: 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.: 9 / 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

-
Non-polymers , 6 types, 1663 molecules

#3: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EBS / 3-ETHYL-2-[(2Z)-2-(3-ETHYL-6-SULFO-1,3-BENZOTHIAZOL-2(3H)-YLIDENE)HYDRAZINO]-6-SULFO-3H-1,3-BENZOTHIAZOL-1-IUM


Mass: 514.619 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N4O6S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1653 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17 % (w/v) PEG MME 5000, 0.1 M sodium acetate, pH 5.5, 0.16 M magnesium formate, 20 mM MgCl2, 8.5 mM 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), protein concentration 8 mg/ml

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.4→49.343 Å / Num. obs: 223121 / % possible obs: 95.5 % / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.033 / Rrim(I) all: 0.067 / Net I/σ(I): 9.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.925 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11468 / CC1/2: 0.589 / Rpim(I) all: 0.542 / Rrim(I) all: 1.079 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZE2

6ze2


Resolution: 1.4→49.343 Å / Cor.coef. Fo:Fc: 0.985 / SU B: 1.659 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.055
Details: Hydrogens have been added in their riding positions. The last refinement cycle was performed against all reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 11066 5 %random selection
Rwork0.1277 223009 --
all0.129 ---
obs0.1291 223009 95.246 %-
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: 19.125 Å2
Baniso -1Baniso -2Baniso -3
1-1.996 Å20 Å2-0 Å2
2---1.229 Å20 Å2
3----0.767 Å2
Refinement stepCycle: LAST / Resolution: 1.4→49.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8917 0 362 1653 10932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01310039
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179147
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.6813874
X-RAY DIFFRACTIONr_angle_other_deg1.5231.59121339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0351323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58220.964498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.971151539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2851579
X-RAY DIFFRACTIONr_chiral_restr0.1060.21382
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211384
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022139
X-RAY DIFFRACTIONr_nbd_refined0.2140.21954
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.28517
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24887
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24075
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.21136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0820.25
X-RAY DIFFRACTIONr_metal_ion_refined0.0040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.217
X-RAY DIFFRACTIONr_nbd_other0.1870.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.256
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1220.21
X-RAY DIFFRACTIONr_mcbond_it1.8191.7094832
X-RAY DIFFRACTIONr_mcbond_other1.8191.7094833
X-RAY DIFFRACTIONr_mcangle_it2.1692.586076
X-RAY DIFFRACTIONr_mcangle_other2.1742.5816077
X-RAY DIFFRACTIONr_scbond_it3.132.195207
X-RAY DIFFRACTIONr_scbond_other3.1182.1875203
X-RAY DIFFRACTIONr_rigid_bond_restr3.358319134
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43600.28617125X-RAY DIFFRACTION99.6973
1.436-1.47600.26316637X-RAY DIFFRACTION99.5274
1.476-1.51800.21216177X-RAY DIFFRACTION99.2941
1.518-1.56500.18615590X-RAY DIFFRACTION98.6709
1.565-1.61600.15715326X-RAY DIFFRACTION99.7397
1.616-1.67300.13514783X-RAY DIFFRACTION99.6428
1.673-1.73600.12214256X-RAY DIFFRACTION99.2136
1.736-1.80700.10913548X-RAY DIFFRACTION98.4593
1.807-1.88700.10313037X-RAY DIFFRACTION98.2146
1.887-1.97900.1188926X-RAY DIFFRACTION70.4332
1.979-2.08600.09511946X-RAY DIFFRACTION98.6376
2.086-2.21200.09311157X-RAY DIFFRACTION97.5348
2.212-2.36500.18017X-RAY DIFFRACTION74.2452
2.365-2.55400.0979765X-RAY DIFFRACTION97.29
2.554-2.79700.1039002X-RAY DIFFRACTION96.9416
2.797-3.12600.1228025X-RAY DIFFRACTION95.1619
3.126-3.60700.1336929X-RAY DIFFRACTION92.5842
3.607-4.41100.1195517X-RAY DIFFRACTION86.7044
4.411-6.21400.1234614X-RAY DIFFRACTION92.2615
6.214-49.34300.1742632X-RAY DIFFRACTION90.1679

+
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