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- PDB-3a64: Crystal structure of CcCel6C, a glycoside hydrolase family 6 enzy... -

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Basic information

Entry
Database: PDB / ID: 3a64
TitleCrystal structure of CcCel6C, a glycoside hydrolase family 6 enzyme, from Coprinopsis cinerea
ComponentsCellobiohydrolase
KeywordsHYDROLASE / seven-stranded beta-alpha barrel / cellulase / glycoside hydrolase family 6 / cellobiohydrolase
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, Y. / Yoshida, M. / Kurakata, Y. / Miyazaki, T. / Nishikawa, A. / Tonozuka, T.
Citation
Journal: Febs J. / Year: 2010
Title: Crystal structure of a glycoside hydrolase family 6 enzyme, CcCel6C, a cellulase constitutively produced by Coprinopsis cinerea
Authors: Liu, Y. / Yoshida, M. / Kurakata, Y. / Miyazaki, T. / Igarashi, K. / Samejima, M. / Fukuda, K. / Nishikawa, A. / Tonozuka, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Heterologous expression, crystallization and preliminary X-ray characterization of CcCel6C, a glycoside hydrolase family 6 enzyme from the basidiomycete Coprinopsis cinerea
Authors: Kurakata, Y. / Tonozuka, T. / Liu, Y. / Kaneko, S. / Nishikawa, A. / Fukuda, K. / Yoshida, M.
#2: Journal: Biosci.Biotechnol.Biochem. / Year: 2009
Title: Characterization of glycoside hydrolase family 6 enzymes from Coprinopsis cinerea
Authors: Liu, Y. / Igarashi, K. / Kaneko, S. / Tonozuka, T. / Samejima, M. / Fukuda, K. / Yoshida, M.
History
DepositionAug 21, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6552
Polymers43,6311
Non-polymers241
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.035, 45.112, 48.904
Angle α, β, γ (deg.)77.81, 87.34, 68.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cellobiohydrolase


Mass: 43631.105 Da / Num. of mol.: 1 / Fragment: UNP residues 20-403
Source method: isolated from a genetically manipulated source
Details: described in Acta Crystallogr. Sect. F, 65, 140-143, 2009
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Strain: 5338 / Gene: CcCel6C / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B7X9Z2, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 8000, 0.1M HEPES-KOH, 0.15M magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.598→50 Å / Num. all: 43370 / Num. obs: 43370 / % possible obs: 95.8 % / Redundancy: 2 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 33.2
Reflection shellResolution: 1.598→1.66 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 9.21 / % possible all: 94

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BVW

1bvw


Resolution: 1.6→19.08 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.214 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16541 4365 10.1 %RANDOM
Rwork0.1406 38982 --
obs0.14309 43347 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 47.19 Å2 / Biso mean: 17.698 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 1 469 3364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222967
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9334058
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4815370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89924.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53115445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2131518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022343
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21490
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22059
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2363
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0510.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5921.51889
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95522987
X-RAY DIFFRACTIONr_scbond_it1.83631235
X-RAY DIFFRACTIONr_scangle_it2.8944.51071
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.598→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 307 -
Rwork0.149 2685 -
all-2992 -
obs--89.69 %

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