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- PDB-2rfw: Crystal Structure of Cellobiohydrolase from Melanocarpus albomyces -

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Basic information

Entry
Database: PDB / ID: 2rfw
TitleCrystal Structure of Cellobiohydrolase from Melanocarpus albomyces
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
Biological speciesMelanocarpus albomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)190,2894
Polymers190,2894
Non-polymers00
Water12,412689
1
A: Cellulose 1,4-beta-cellobiosidase


Theoretical massNumber of molelcules
Total (without water)47,5721
Polymers47,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulose 1,4-beta-cellobiosidase


Theoretical massNumber of molelcules
Total (without water)47,5721
Polymers47,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cellulose 1,4-beta-cellobiosidase


Theoretical massNumber of molelcules
Total (without water)47,5721
Polymers47,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cellulose 1,4-beta-cellobiosidase


Theoretical massNumber of molelcules
Total (without water)47,5721
Polymers47,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.940, 94.520, 189.850
Angle α, β, γ (deg.)90.000, 90.000, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% 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: X12 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2006
RadiationMonochromator: horizontally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 235645 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 0.072 / Net I/σ(I): 13.6
Reflection shellResolution: 1.6→1.7 Å / Mean I/σ(I) obs: 4.8 / Rsym value: 0.302 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Num. parameters: 56088 / Num. restraintsaints: 55954 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: Used twinning operator h, -k, -l
RfactorNum. reflection% reflectionSelection details
Rfree0.243 11779 5.3 %THIN RESOLUTION SHELLS
all0.199 223822 --
obs0.199 223822 94.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Displacement parametersBiso mean: 21.628 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13332 0 0 689 14021
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.102
X-RAY DIFFRACTIONs_approx_iso_adps0

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