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- PDB-3voi: CcCel6A catalytic domain complexed with p-nitrophenyl beta-D-cell... -

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Basic information

Entry
Database: PDB / ID: 3voi
TitleCcCel6A catalytic domain complexed with p-nitrophenyl beta-D-cellotrioside
ComponentsCellobiohydrolase
KeywordsHYDROLASE / Seven-stranded beta-alpha barrel / 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 binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region / metal ion binding
Similarity search - Function
1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 2. / 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 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily ...1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 2. / 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 / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-RCB / Glucanase
Similarity search - Component
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTamura, M. / Miyazaki, T. / Tanaka, Y. / Yoshida, M. / Nishikawa, A. / Tonozuka, T.
CitationJournal: Febs J. / Year: 2012
Title: Comparison of the structural changes in two cellobiohydrolases, CcCel6A and CcCel6C, from Coprinopsis cinerea - a tweezer-like motion in the structure of CcCel6C
Authors: Tamura, M. / Miyazaki, T. / Tanaka, Y. / Yoshida, M. / Nishikawa, A. / Tonozuka, T.
History
DepositionJan 24, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Nov 8, 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7244
Polymers41,0501
Non-polymers6743
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.973, 71.502, 101.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cellobiohydrolase


Mass: 41049.859 Da / Num. of mol.: 1 / Fragment: UNP residues 93-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Strain: 5338 / Gene: CcCel6A / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B7X9Z0, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-RCB / 4-nitrophenyl beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranoside / p-nitrophenyl beta-D-cellotrioside


Mass: 625.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H35NO18
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 8000, 0.1M HEPES-KOH, 0.1M magnesium acetate, pH 7, 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 210r / Detector: CCD / Date: Jun 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22349 / % possible obs: 95.1 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 29.5
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 8.3 / % possible all: 96.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VOH

3voh


Resolution: 2→30.72 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25222 1128 5.1 %RANDOM
Rwork0.19383 ---
obs0.19672 20940 95.08 %-
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 mean: 17.542 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→30.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 45 245 3076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222907
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9633966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7735361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31624.088137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39915438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2321520
X-RAY DIFFRACTIONr_chiral_restr0.0730.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212259
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4741.51793
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.922867
X-RAY DIFFRACTIONr_scbond_it1.64131114
X-RAY DIFFRACTIONr_scangle_it2.6324.51098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 89 -
Rwork0.287 1534 -
obs--97.83 %

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