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- PDB-9k7m: Coprinopsis cinerea GH131 protein CcGH131B E161A in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9k7m
TitleCoprinopsis cinerea GH131 protein CcGH131B E161A in complex with cellobiose
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 / alpha-cellobiose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glycoside hydrolase 131 catalytic N-terminal domain-containing protein
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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.Glyosci. / 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
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year

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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)71,6558
Polymers70,3232
Non-polymers1,3316
Water16,412911
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A: Glycoside hydrolase 131 catalytic N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8054
Polymers35,1621
Non-polymers6443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint5 kcal/mol
Surface area13660 Å2
MethodPISA
2
B: Glycoside hydrolase 131 catalytic N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8494
Polymers35,1621
Non-polymers6883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint5 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.660, 71.660, 226.521
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein / Sugars , 2 types, 4 molecules AB

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


Mass: 35161.672 Da / Num. of mol.: 2 / Mutation: T87A/E161A/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. The potential catalatic residue Glu161 is replaced with Ala.
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: Polysaccharide beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 915 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, ammonium phosphate, MES-NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→48 Å / Num. obs: 115588 / % possible obs: 99.7 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.026 / Net I/σ(I): 16.9
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 16824 / Rpim(I) all: 0.146 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→35.83 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18185 5926 5.1 %RANDOM
Rwork0.15873 ---
obs0.15993 109564 99.62 %-
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: 15.501 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.45→35.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4790 0 87 911 5788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125023
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164650
X-RAY DIFFRACTIONr_angle_refined_deg1.381.6686875
X-RAY DIFFRACTIONr_angle_other_deg0.7631.58810722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7025602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.657530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06610744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025846
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021146
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_it1.4461.5682414
X-RAY DIFFRACTIONr_mcbond_other1.4411.5682414
X-RAY DIFFRACTIONr_mcangle_it2.3532.8183014
X-RAY DIFFRACTIONr_mcangle_other2.3532.8193015
X-RAY DIFFRACTIONr_scbond_it1.8371.8082609
X-RAY DIFFRACTIONr_scbond_other1.8371.812610
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9933.2193862
X-RAY DIFFRACTIONr_long_range_B_refined5.0721.715802
X-RAY DIFFRACTIONr_long_range_B_other4.70717.785492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 422 -
Rwork0.219 8081 -
obs--99.03 %

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