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- PDB-2rg0: Crystal structure of cellobiohydrolase from Melanocarpus albomyce... -

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Basic information

Entry
Database: PDB / ID: 2rg0
TitleCrystal structure of cellobiohydrolase from Melanocarpus albomyces complexed with cellotetraose
ComponentsCellulose 1,4-beta-cellobiosidase
KeywordsHYDROLASE / Glycosidase
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-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
beta-cellobiose / beta-cellotetraose / Glucanase
Similarity search - Component
Biological speciesMelanocarpus albomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsParkkinen, T. / Koivula, A. / Vehmaanper, J. / Rouvinen, J.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structures of Melanocarpus albomyces cellobiohydrolase Cel7B in complex with cello-oligomers show high flexibility in the substrate binding
Authors: Parkkinen, T. / Koivula, A. / Rouvinen, J.
History
DepositionOct 2, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 1, 2018Group: Data collection / Structure summary / Category: diffrn_source / entity
Item: _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_mutation
Revision 1.3Aug 15, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.pdbx_mutation / _entity.src_method
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellulose 1,4-beta-cellobiosidase
B: Cellulose 1,4-beta-cellobiosidase
C: Cellulose 1,4-beta-cellobiosidase
D: Cellulose 1,4-beta-cellobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,66710
Polymers190,2894
Non-polymers2,3786
Water8,359464
1
A: Cellulose 1,4-beta-cellobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2573
Polymers47,5721
Non-polymers6852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulose 1,4-beta-cellobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2392
Polymers47,5721
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cellulose 1,4-beta-cellobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9152
Polymers47,5721
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cellulose 1,4-beta-cellobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2573
Polymers47,5721
Non-polymers6852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.980, 94.810, 190.430
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cellulose 1,4-beta-cellobiosidase


Mass: 47572.230 Da / Num. of mol.: 4 / Mutation: Q1(PCA)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melanocarpus albomyces (fungus) / Production host: Trichoderma reesei (fungus)
References: UniProt: Q8J0K6, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


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


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG8000, 0.1M calcium chloride, 0.1M cacodylate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8162 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8162 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 105275 / Num. obs: 105275 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.8 Å2 / Rsym value: 0.177 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.453 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Num. parameters: 55836 / Num. restraintsaints: 57366 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: Used twin operator h, -k, -l
RfactorNum. reflection% reflectionSelection details
Rfree0.282 5260 5.3 %THIN RESOLUTION SHELLS
obs0.211 99948 94.6 %-
all-99948 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Displacement parametersBiso mean: 32.843 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13332 0 160 464 13956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_zero_chiral_vol0.021
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.109
X-RAY DIFFRACTIONs_approx_iso_adps0

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