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- PDB-8w4y: Neutron structure of cellulase Cel6A from Phanerochaete chrysospo... -

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Basic information

Entry
Database: PDB / ID: 8w4y
TitleNeutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature, low-D2O-solvent
ComponentsGlucanase
KeywordsHYDROLASE / Cellulase / Glycoside hydrolase family 6 / Cellobiohydrolase II
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 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain ...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 / 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
Similarity search - Domain/homology
Biological speciesPhanerodontia chrysosporium (fungus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTachioka, M. / Yamaguchi, S. / Nakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Yano, N. / Chatake, T. / Tamada, T. / Takeda, K. ...Tachioka, M. / Yamaguchi, S. / Nakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Yano, N. / Chatake, T. / Tamada, T. / Takeda, K. / Niwa, S. / Tanaka, H. / Takahashi, S. / Inaka, K. / Furubayashi, N. / Deguchi, S. / Samejima, M. / Igarashi, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H05494 Japan
Japan Society for the Promotion of Science (JSPS)23H00341, 19H03013, 18J01906, 15J10657 Japan
CitationJournal: To Be Published
Title: Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase
Authors: Tachioka, M. / Yamaguchi, S. / Nakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Yano, N. / Chatake, T. / Tamada, T. / Takeda, K. / Niwa, S. / Tanaka, H. / Takahashi, S. / Inaka, K. / ...Authors: Tachioka, M. / Yamaguchi, S. / Nakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Yano, N. / Chatake, T. / Tamada, T. / Takeda, K. / Niwa, S. / Tanaka, H. / Takahashi, S. / Inaka, K. / Furubayashi, N. / Deguchi, S. / Samejima, M. / Igarashi, K.
History
DepositionAug 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucanase


Theoretical massNumber of molelcules
Total (without water)38,3821
Polymers38,3821
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14210 Å2
Unit cell
Length a, b, c (Å)55.350, 67.920, 89.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glucanase


Mass: 38381.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerodontia chrysosporium (fungus) / Gene: cel6A / Production host: Komagataella pastoris (fungus) / References: UniProt: H3K419
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: polyethylene glycol 3350, sodium chloride, 2-methyl-2,4-pentandiol, acetate buffer,
PH range: 5.2-5.7

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12981N
22981N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NE3A11
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0322.9-5.6
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M1PIXELApr 16, 2017
iBIX2DIFFRACTOMETERFeb 5, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.91
35.61
Reflection

Entry-ID: 8W4Y

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.4-1006535296.96.712.520.075123.3
2.15-20.91887591.22.20.28926.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsDiffraction-ID
1.4-1.420.43231761
2.15-2.230.5421082

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158phasing
STARGazerdata reduction
Refinement

SU ML: 0.117 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 15.6354 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)Diffraction-ID
1.4-47.12X-RAY DIFFRACTION20.290.16350.14520.1461329061998652965.0496.921.37
2.15-20.4NEUTRON DIFFRACTION0.17670.15541812494.732
Refinement stepCycle: LAST / Resolution: 1.4→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 0 246 2956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01142955
X-RAY DIFFRACTIONf_angle_d1.04374076
X-RAY DIFFRACTIONf_chiral_restr0.0813452
X-RAY DIFFRACTIONf_plane_restr0.0085549
X-RAY DIFFRACTIONf_dihedral_angle_d14.37381052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.24321230.22652508X-RAY DIFFRACTION94.4
1.42-1.440.22151520.20412476X-RAY DIFFRACTION95.15
1.44-1.460.2171280.19492510X-RAY DIFFRACTION95.1
1.46-1.490.23121510.19222485X-RAY DIFFRACTION95.13
1.49-1.510.23461140.18812520X-RAY DIFFRACTION95.54
1.51-1.540.22481450.1872507X-RAY DIFFRACTION95.36
1.54-1.570.181430.19132506X-RAY DIFFRACTION95.84
1.57-1.60.19251260.17622548X-RAY DIFFRACTION96.19
1.6-1.640.20241490.18222541X-RAY DIFFRACTION96.24
1.64-1.680.20081240.17012563X-RAY DIFFRACTION96.31
1.68-1.720.20091060.1682575X-RAY DIFFRACTION96.37
1.72-1.760.19511360.16842536X-RAY DIFFRACTION96.71
1.76-1.820.17831320.15752572X-RAY DIFFRACTION96.88
1.82-1.870.1721710.15342546X-RAY DIFFRACTION97.11
1.87-1.940.1831420.16212593X-RAY DIFFRACTION97.12
1.94-2.020.15691350.14962572X-RAY DIFFRACTION97.83
2.02-2.110.15561430.14662604X-RAY DIFFRACTION97.45
2.11-2.220.17271420.13722609X-RAY DIFFRACTION98.29
2.22-2.360.12241180.13592653X-RAY DIFFRACTION97.92
2.36-2.540.15161260.13592649X-RAY DIFFRACTION98.47
2.54-2.80.14831510.13432654X-RAY DIFFRACTION98.8
2.8-3.20.15891330.13642695X-RAY DIFFRACTION98.92
3.21-4.040.14061500.11182716X-RAY DIFFRACTION99.07
4.04-47.120.13631500.12322860X-RAY DIFFRACTION99.47

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