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- PDB-4i5u: Crystal structure of a fungal chimeric cellobiohydrolase Cel6A -

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Basic information

Entry
Database: PDB / ID: 4i5u
TitleCrystal structure of a fungal chimeric cellobiohydrolase Cel6A
ComponentsChimeric cel6A
KeywordsHYDROLASE / cellobiohydrolase / chimera protein / glycoside hydrolase
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / 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 / identical protein binding
Similarity search - Function
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 / 1, 4-beta cellobiohydrolase / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily ...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 / 1, 4-beta cellobiohydrolase / 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
ACETATE ION / TRIETHYLENE GLYCOL / Exoglucanase 2 / Glucanase / Exoglucanase-6A
Similarity search - Component
Biological speciesHumicola insolens (fungus)
Chaetomium thermophilum (fungus)
Trichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.22 Å
AuthorsArnold, F.H. / Wu, I.
CitationJournal: Biotechnol.Bioeng. / Year: 2013
Title: Engineered thermostable fungal Cel6A and Cel7A cellobiohydrolases hydrolyze cellulose efficiently at elevated temperatures.
Authors: Wu, I. / Arnold, F.H.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimeric cel6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,97316
Polymers39,7401
Non-polymers1,23315
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.599, 45.414, 58.194
Angle α, β, γ (deg.)90.000, 95.470, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-653-

HOH

21A-753-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chimeric cel6A / 1 / 4-beta-cellobiohydrolase 6A / Avicelase 2 / Beta-glucancellobiohydrolase 6A / ...1 / 4-beta-cellobiohydrolase 6A / Avicelase 2 / Beta-glucancellobiohydrolase 6A / Exocellobiohydrolase 6A / 4-beta-cellobiohydrolase / Exocellobiohydrolase II / CBHII / Exoglucanase II


Mass: 39740.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Humicola insolens (fungus), (gene. exp.) Chaetomium thermophilum (fungus), (gene. exp.) Trichoderma reesei (fungus)
Gene: avi2, cel6A, cbh2 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q9C1S9, UniProt: P07987, UniProt: Q5G2D4, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Non-polymers , 5 types, 342 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE 90-134 ARE FROM HUMICOLA INSOLENS CEL6A. RESIDUE 135-308 AND 401-447 ARE FROM HYPOCREA ...RESIDUE 90-134 ARE FROM HUMICOLA INSOLENS CEL6A. RESIDUE 135-308 AND 401-447 ARE FROM HYPOCREA JECORINA CEL6A. RESIDUE 309-400 ARE FROM CHAETOMIUM THERMOPHILUM CEL6A.

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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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.22→35.308 Å / Num. all: 106851 / Num. obs: 106851 / % possible obs: 87.3 % / Redundancy: 2.1 % / Rsym value: 0.027 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.22-1.291.90.2153.624424126700.21571.2
1.29-1.3620.1664.730030147400.16687.7
1.36-1.4620.1156.828965141320.11589.3
1.46-1.572.10.07710.127819134790.07791.6
1.57-1.732.10.05314.325769123310.05390.9
1.73-1.932.10.03620.523921113540.03692.3
1.93-2.232.10.02427.62065598440.02490.4
2.23-2.732.10.02130.91758183350.02190.6
2.73-3.862.10.01832.71358664420.01889.6
3.86-35.3082.10.01733.1734435240.01787.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→35.308 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.1576 / WRfactor Rwork: 0.1424 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9289 / SU B: 0.875 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0354 / SU Rfree: 0.0368 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1584 5345 5 %RANDOM
Rwork0.1426 ---
obs0.1434 106847 86.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.5 Å2 / Biso mean: 13.267 Å2 / Biso min: 3.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å2-0.51 Å2
2---0.09 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.22→35.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 76 327 3147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.022995
X-RAY DIFFRACTIONr_bond_other_d0.0030.0227
X-RAY DIFFRACTIONr_angle_refined_deg2.6141.9594100
X-RAY DIFFRACTIONr_angle_other_deg2.729358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.565389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.30624.964137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85715415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5671512
X-RAY DIFFRACTIONr_chiral_restr0.1440.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0222369
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 247 -
Rwork0.194 5063 -
all-5310 -
obs--58.99 %
Refinement TLS params.Method: refined / Origin x: -19.7107 Å / Origin y: -22.6784 Å / Origin z: 11.898 Å
111213212223313233
T0.0137 Å20.0001 Å20.0032 Å2-0.0072 Å2-0.0003 Å2--0.008 Å2
L0.223 °2-0.0228 °20.1417 °2-0.1075 °20.0139 °2--0.1197 °2
S-0.0045 Å °0.002 Å °0.0066 Å °0.0046 Å °-0.0035 Å °0.0208 Å °0.0016 Å °0.0123 Å °0.008 Å °

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