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- PDB-4b4h: Thermobifida fusca cellobiohydrolase Cel6B(E3) catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4b4h
TitleThermobifida fusca cellobiohydrolase Cel6B(E3) catalytic domain
ComponentsBETA-1,4-EXOCELLULASE
KeywordsHYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDE HYDROLASE FAMILY 6 / CELLULASE / CELLOBIOHYDROLASE
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / polysaccharide binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
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 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II ...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 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesTHERMOBIFIDA FUSCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSandgren, M. / Wu, M. / Stahlberg, J. / Karkehabadi, S. / Mitchinson, C. / Kelemen, B.R. / Larenas, E.A. / Hansson, H.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: The Structure of a Bacterial Cellobiohydrolase: The Catalytic Core of the Thermobifida Fusca Family Gh6 Cellobiohydrolase Cel6B.
Authors: Sandgren, M. / Wu, M. / Karkehabadi, S. / Mitchinson, C. / Kelemen, B.R. / Larenas, E.A. / Stahlberg, J. / Hansson, H.
History
DepositionJul 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 16, 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: BETA-1,4-EXOCELLULASE
B: BETA-1,4-EXOCELLULASE


Theoretical massNumber of molelcules
Total (without water)90,9482
Polymers90,9482
Non-polymers00
Water14,790821
1
A: BETA-1,4-EXOCELLULASE


Theoretical massNumber of molelcules
Total (without water)45,4741
Polymers45,4741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-1,4-EXOCELLULASE


Theoretical massNumber of molelcules
Total (without water)45,4741
Polymers45,4741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.750, 93.350, 96.590
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-1,4-EXOCELLULASE / CEL6B


Mass: 45473.750 Da / Num. of mol.: 2 / Fragment: RESIDUES 177-596
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOBIFIDA FUSCA (bacteria) / Plasmid: PSEQCT / Production host: STREPTOMYCES LIVIDANS (bacteria)
References: UniProt: Q60029, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / 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: 2.1 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 4
Details: 20% PEG6000, 0.1 M SODIUM CITRATE AT PH 4.0, 1 M LITHIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.515
11h,-k,-l20.485
ReflectionResolution: 1.5→26.5 Å / Num. obs: 106191 / % possible obs: 87.7 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.2
Reflection shellResolution: 1.5→1.8 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7.9 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1QK2, 2BVW, 1UP0, 1TML AND 1DYS

1qk2

2bvw

1up0

1tml

1dys


Resolution: 1.5→39.09 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.863 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23226 5475 5.1 %RANDOM
Rwork0.1957 ---
obs0.1976 102690 89.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.208 Å2
Baniso -1Baniso -2Baniso -3
1--3.37 Å20 Å20.89 Å2
2---10.86 Å20 Å2
3---14.23 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6328 0 0 821 7149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9419043
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9124.702336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52315964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0441543
X-RAY DIFFRACTIONr_chiral_restr0.0830.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215339
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 424 -
Rwork0.212 7149 -
obs--85.57 %

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