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- PDB-6jt5: Crystal structure of PQQ doamin of Pyranose Dehydrogenase from Co... -

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Basic information

Entry
Database: PDB / ID: 6jt5
TitleCrystal structure of PQQ doamin of Pyranose Dehydrogenase from Coprinopsis cinerea: apo-from
ComponentsExtracellular PQQ-dependent sugar dehydrogenase
KeywordsOXIDOREDUCTASE / pyrroloquinoline quinone / sugar dehydrogenase / AA family 12
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With unknown physiological acceptors / cellulose binding / carbohydrate metabolic process / oxidoreductase activity / extracellular region / metal ion binding
Similarity search - Function
: / TrAA12-like / DOMON domain / Possible catecholamine-binding domain present in a variety of eukaryotic proteins. / Cellobiose dehydrogenase, cytochrome domain / Cytochrome domain of cellobiose dehydrogenase / Soluble quinoprotein glucose/sorbosone dehydrogenase / TolB, C-terminal domain / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal ...: / TrAA12-like / DOMON domain / Possible catecholamine-binding domain present in a variety of eukaryotic proteins. / Cellobiose dehydrogenase, cytochrome domain / Cytochrome domain of cellobiose dehydrogenase / Soluble quinoprotein glucose/sorbosone dehydrogenase / TolB, C-terminal domain / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / TRIETHYLENE GLYCOL / Pyrroloquinoline quinone-dependent pyranose dehydrogenase / Pyrroloquinoline quinone-dependent pyranose dehydrogenase
Similarity search - Component
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsTakeda, K. / Ishida, T. / Yoshida, M. / Samejima, M. / Ohno, H. / Igarashi, K. / Nakamura, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K17703 Japan
CitationJournal: Appl.Environ.Microbiol. / Year: 2019
Title: Crystal Structure of the Catalytic and CytochromebDomains in a Eukaryotic Pyrroloquinoline Quinone-Dependent Dehydrogenase.
Authors: Takeda, K. / Ishida, T. / Yoshida, M. / Samejima, M. / Ohno, H. / Igarashi, K. / Nakamura, N.
History
DepositionApr 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Feb 12, 2020Group: Data collection / Structure summary / Category: chem_comp / struct_keywords / Item: _chem_comp.type / _struct_keywords.text
Revision 1.3Apr 15, 2020Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular PQQ-dependent sugar dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9128
Polymers45,1741
Non-polymers7387
Water13,962775
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-9 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.298, 47.851, 69.375
Angle α, β, γ (deg.)90.00, 115.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Extracellular PQQ-dependent sugar dehydrogenase


Mass: 45173.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Gene: CcSDH / Production host: Komagataella pastoris (fungus) / Variant (production host): KM71H / References: UniProt: A0A0A8IDB7, UniProt: A8P0V4*PLUS
#2: 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.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 6 types, 781 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 5mM sodium acetate, 0.2M sodium formate, 20% PEG 3350, 20mM calcium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 60275 / % possible obs: 99.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.081 / Net I/av σ(I): 17.4 / Net I/σ(I): 32.9
Reflection shellResolution: 1.5→1.59 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.5→19.75 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.134 2955 5 %
Rwork0.105 --
obs0.107 56135 99.59 %
Refinement stepCycle: LAST / Resolution: 1.5→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 45 775 3997
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.145 210 -
Rwork0.109 3980 -
obs--96.59 %

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