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- PDB-9k7o: Coprinopsis cinerea GH131 protein CcGH131B -

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Basic information

Entry
Database: PDB / ID: 9k7o
TitleCoprinopsis cinerea GH131 protein CcGH131B
ComponentsGlycoside hydrolase 131 catalytic N-terminal domain-containing protein
KeywordsHYDROLASE / Coprinopsis cinerea / GH131 / cellobiose / cellulose
Function / homologyGlycoside hydrolase 131, catalytic N-terminal / Glycoside hydrolase 131 catalytic N-terminal domain / DI(HYDROXYETHYL)ETHER / Glycoside hydrolase 131 catalytic N-terminal domain-containing protein
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShiojima, Y. / Tonozuka, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K08698 Japan
Japan Science and TechnologyJPMJSP2116 Japan
CitationJournal: J Appl Glycosci (1999) / Year: 2025
Title: Crystal Structure of CcGH131B, a Protein Belonging to Glycoside Hydrolase Family 131 from the Basidiomycete Coprinopsis cinerea .
Authors: Shiojima, Y. / Sano, R. / Kozono, T. / Nishikawa, A. / Kojima, Y. / Yoshida, M. / Sunagawa, N. / Igarashi, K. / Tonozuka, T.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Structure summary
Category: audit_author / citation_author / pdbx_contact_author
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _pdbx_contact_author.name_first / _pdbx_contact_author.name_last
Revision 1.2Apr 16, 2025Group: Database references / Category: citation / citation_author
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Revision 1.3Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase 131 catalytic N-terminal domain-containing protein
B: Glycoside hydrolase 131 catalytic N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6524
Polymers70,4392
Non-polymers2122
Water8,251458
1
A: Glycoside hydrolase 131 catalytic N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3262
Polymers35,2201
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase 131 catalytic N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3262
Polymers35,2201
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.849, 71.849, 225.802
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Glycoside hydrolase 131 catalytic N-terminal domain-containing protein


Mass: 35219.707 Da / Num. of mol.: 2 / Mutation: T87A/K247E
Source method: isolated from a genetically manipulated source
Details: The original protein name: CC1G_15039 The original N-terminal signal peptide is removed in the expression vector. Met is artificially placed at the N-terminus, and C-terminal tag sequence is ...Details: The original protein name: CC1G_15039 The original N-terminal signal peptide is removed in the expression vector. Met is artificially placed at the N-terminus, and C-terminal tag sequence is AAALEHHHHHH. In the sequence of CC1G_15039 in the databese, the 87th and the 247th residues are Thr and Lys, while these residues are Ala and Glu, respectively, in this study.
Source: (gene. exp.) Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (fungus)
Gene: CC1G_15039 / Production host: Escherichia coli (E. coli) / References: UniProt: D6RP27
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 10000, PEG 20000, MES-NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.9 Å / Num. obs: 51549 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.041 / Net I/σ(I): 28.6
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4 / Num. unique obs: 5122 / Rpim(I) all: 0.159

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21575 2412 4.7 %RANDOM
Rwork0.1799 ---
obs0.18164 49044 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.388 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4793 0 14 458 5265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124951
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164587
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.6566773
X-RAY DIFFRACTIONr_angle_other_deg0.7621.57810561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8295601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.32530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75310748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025847
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021145
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5392.942410
X-RAY DIFFRACTIONr_mcbond_other2.5392.942410
X-RAY DIFFRACTIONr_mcangle_it3.8225.2783009
X-RAY DIFFRACTIONr_mcangle_other3.8215.2793010
X-RAY DIFFRACTIONr_scbond_it2.8343.2252541
X-RAY DIFFRACTIONr_scbond_other2.8333.2252542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3655.8083765
X-RAY DIFFRACTIONr_long_range_B_refined6.32932.495511
X-RAY DIFFRACTIONr_long_range_B_other6.29731.675410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 147 -
Rwork0.268 3537 -
obs--96.47 %

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