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- PDB-5xcy: Structure of the cellobiohydrolase Cel6A from Phanerochaete chrys... -

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Basic information

Entry
Database: PDB / ID: 5xcy
TitleStructure of the cellobiohydrolase Cel6A from Phanerochaete chrysosporium at 1.2 angstrom
ComponentsGlucanase
KeywordsHYDROLASE / Glycoside hydrolase family 6
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
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
Glucanase / Glucanase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.199 Å
AuthorsTachioka, M. / Nakamura, A. / Ishida, T. / Igarashi, K. / Samejima, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japanese Ministry of Education, Culture, Sports, and Technology24114001 Japan
Japanese Ministry of Education, Culture, Sports, and Technology24114008 Japan
Japan Society for the Promotion of Science24380089 Japan
Japan Society for the Promotion of Science15J10657 Japan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of a family 6 cellobiohydrolase from the basidiomycete Phanerochaete chrysosporium
Authors: Tachioka, M. / Nakamura, A. / Ishida, T. / Igarashi, K. / Samejima, M.
History
DepositionMar 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucanase


Theoretical massNumber of molelcules
Total (without water)38,3821
Polymers38,3821
Non-polymers00
Water8,845491
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14200 Å2
Unit cell
Length a, b, c (Å)54.712, 67.180, 89.113
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 Glucanase


Mass: 38381.574 Da / Num. of mol.: 1 / Fragment: UNP residues 82-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Gene: cel6A / Production host: Komagataella pastoris (fungus)
References: UniProt: H3K419, UniProt: Q02321*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: polyethylene glycol 3350, 2-methyl-2,4-pentandiol, calcium acetate, acetate buffer,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.199→50 Å / Num. obs: 103410 / % possible obs: 99.8 % / Redundancy: 3.1 % / Net I/σ(I): 43.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.199→31.431 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 12.82
RfactorNum. reflection% reflection
Rfree0.1577 5162 5 %
Rwork0.1381 --
obs0.1391 103213 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.199→31.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 0 0 491 3200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053139
X-RAY DIFFRACTIONf_angle_d0.8314349
X-RAY DIFFRACTIONf_dihedral_angle_d3.0311624
X-RAY DIFFRACTIONf_chiral_restr0.078476
X-RAY DIFFRACTIONf_plane_restr0.006593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.199-1.21260.19831470.1573072X-RAY DIFFRACTION96
1.2126-1.22680.20051910.14683219X-RAY DIFFRACTION100
1.2268-1.24180.17711750.1443280X-RAY DIFFRACTION100
1.2418-1.25750.19531610.1353219X-RAY DIFFRACTION100
1.2575-1.27410.16011880.13243230X-RAY DIFFRACTION100
1.2741-1.29150.18091630.12963256X-RAY DIFFRACTION100
1.2915-1.310.15391770.12753224X-RAY DIFFRACTION100
1.31-1.32950.14541910.12773219X-RAY DIFFRACTION100
1.3295-1.35030.16661450.13253274X-RAY DIFFRACTION100
1.3503-1.37240.15051640.13023258X-RAY DIFFRACTION100
1.3724-1.39610.14051830.1273264X-RAY DIFFRACTION100
1.3961-1.42150.17061690.12793206X-RAY DIFFRACTION100
1.4215-1.44880.15391530.12233266X-RAY DIFFRACTION100
1.4488-1.47840.14831560.12233285X-RAY DIFFRACTION100
1.4784-1.51060.15561800.1173231X-RAY DIFFRACTION100
1.5106-1.54570.13151810.11623241X-RAY DIFFRACTION100
1.5457-1.58440.14171760.1153268X-RAY DIFFRACTION100
1.5844-1.62720.12711720.12313259X-RAY DIFFRACTION100
1.6272-1.67510.14561570.12673272X-RAY DIFFRACTION100
1.6751-1.72910.16891720.13253271X-RAY DIFFRACTION100
1.7291-1.79090.16381660.14143277X-RAY DIFFRACTION100
1.7909-1.86260.16241820.14013286X-RAY DIFFRACTION100
1.8626-1.94740.15871660.14653284X-RAY DIFFRACTION100
1.9474-2.050.16471600.14313300X-RAY DIFFRACTION100
2.05-2.17840.1691720.13963322X-RAY DIFFRACTION100
2.1784-2.34660.16681850.14343278X-RAY DIFFRACTION100
2.3466-2.58260.17231520.1543332X-RAY DIFFRACTION100
2.5826-2.95610.17431710.1543340X-RAY DIFFRACTION100
2.9561-3.72340.14942050.14113350X-RAY DIFFRACTION100
3.7234-31.4420.14032020.13673468X-RAY DIFFRACTION99

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