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- PDB-6jwf: Holo form of Pyranose Dehydrogenase PQQ domain from Coprinopsis c... -

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Basic information

Entry
Database: PDB / ID: 6jwf
TitleHolo form of Pyranose Dehydrogenase PQQ domain from Coprinopsis cinerea
ComponentsExtracellular PQQ-dependent sugar dehydrogenase
KeywordsOXIDOREDUCTASE / pyrroloquinoline quinone / sugar dehydrogenase / AA family 12
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
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 / 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. ...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 / 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
Similarity search - Domain/homology
ACETATE ION / PYRROLOQUINOLINE QUINONE / Extracellular PQQ-dependent sugar dehydrogenase / CBM1 domain-containing protein
Similarity search - Component
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
Citation
Journal: 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.
#1: Journal: To Be Published
Title: The first crystal structure of the catalytic domain and the cytochrome b domain in a eukaryotic PQQ-dependent dehydrogenase
Authors: Takeda, K. / Ishida, T. / Yoshida, M. / Samejima, M. / Ohno, H. / Igarashi, K. / Nakamura, N.
History
DepositionApr 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Extracellular PQQ-dependent sugar dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,11120
Polymers90,3482
Non-polymers1,76318
Water27,3831520
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A: Extracellular PQQ-dependent sugar dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,03511
Polymers45,1741
Non-polymers86110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-18 kcal/mol
Surface area15780 Å2
MethodPISA
2
B: Extracellular PQQ-dependent sugar dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0769
Polymers45,1741
Non-polymers9028
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-16 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.330, 95.638, 106.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Extracellular PQQ-dependent sugar dehydrogenase / pyranose dehydrogenase


Mass: 45173.996 Da / Num. of mol.: 2 / Fragment: PQQ dependent catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Gene: CcSDH / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: UniProt: A0A0A8IDB7, UniProt: A8P0V4*PLUS
#6: 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 / N-Acetylglucosamine


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 , 5 types, 1537 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE / Pyrroloquinoline quinone


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1520 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 5 / Details: 5mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. obs: 213104 / % possible obs: 99.4 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.99 / Num. unique obs: 33130 / CC1/2: 0.863 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JT5

6jt5


Resolution: 1.3→71.07 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.177 10656 5 %Random selection
Rwork0.1595 ---
obs0.16 202449 99.38 %-
Refinement stepCycle: LAST / Resolution: 1.3→71.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 116 1520 7990
LS refinement shellResolution: 1.297→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 722 -
Rwork0.245 13706 -
obs--91.89 %

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