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- PDB-8zik: Crystal structure of a beta-1,4-endoglucanase from Bispora sp. ME... -

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Basic information

Entry
Database: PDB / ID: 8zik
TitleCrystal structure of a beta-1,4-endoglucanase from Bispora sp. MEY-1 in complex with cellotetraose
Componentscellulase
KeywordsHYDROLASE / Promiscuous cellulase in complex with sugars
Function / homologyglucan catabolic process / cellulase / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / cellulase
Function and homology information
Biological speciesBispora sp. MEY-1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsZheng, J. / Luo, H.Y. / Yao, B. / Tian, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31872395 China
CitationJournal: To Be Published
Title: Unraveling the Key Determinants of Substrate Promiscuity in Glycoside Hydrolase Family 5_5 Cellulases
Authors: Zheng, J. / Luo, H.Y.
History
DepositionMay 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: cellulase
B: cellulase
A: cellulase
C: cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,38027
Polymers141,6204
Non-polymers7,76023
Water17,619978
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.318, 94.990, 179.759
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
cellulase


Mass: 35404.938 Da / Num. of mol.: 4 / Mutation: E142Q,E257Q
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Bispora sp. MEY-1 (species) (554688) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A150VE32.
Source: (gene. exp.) Bispora sp. MEY-1 (fungus) / Gene: M433DRAFT_60941 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A150VE32, cellulase
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 6 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris, pH 7.5, 0.2 M sodium acetate, 32% PEG 4000

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.87→29.86 Å / Num. obs: 92829 / % possible obs: 90.15 % / Redundancy: 10.3 % / Biso Wilson estimate: 26.19 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.04 / Rrim(I) all: 0.136 / Χ2: 1.077 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.87-1.94.50.85932230.6940.9050.380.9450.84263.3
1.9-1.944.80.79834950.760.9290.3450.8750.8769.1
1.94-1.975.40.78837680.8030.9440.3180.8540.91474.5
1.97-2.016.50.75338790.8580.9610.2820.8070.92776.2
2.01-2.067.10.70440640.9050.9750.2510.750.95579.8
2.06-2.117.70.64741500.9180.9780.2250.6870.98882.3
2.11-2.168.20.60743210.9350.9830.2070.6441.02885
2.16-2.228.60.55744700.9390.9840.1880.591.03587.8
2.22-2.289.40.54147650.9590.990.1750.5711.07694.1
2.28-2.3610.10.49949560.9710.9920.1580.5241.0797.1
2.36-2.4411.20.46250980.9820.9950.1420.4841.09499.7
2.44-2.5411.70.40251020.9820.9950.1220.421.10999.9
2.54-2.6512.50.33751160.990.9970.0990.3521.174100
2.65-2.7912.90.26251180.9930.9980.0750.2731.223100
2.79-2.9712.90.19551290.9960.9990.0570.2031.266100
2.97-3.212.80.12951510.9970.9990.0380.1351.115100
3.2-3.5213.40.09551790.99910.0270.0991.018100
3.52-4.0312.60.0751980.99910.0210.0731.103100
4.03-5.0713.10.06252470.99910.0180.0651.008100
5.07-1012.30.06754890.99810.020.071.006100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→29.86 Å / SU ML: 0.2439 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2391 4590 4.95 %
Rwork0.1882 88068 -
obs0.1908 92658 90.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.19 Å2
Refinement stepCycle: LAST / Resolution: 1.87→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9468 0 508 978 10954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007410234
X-RAY DIFFRACTIONf_angle_d0.966714005
X-RAY DIFFRACTIONf_chiral_restr0.0591617
X-RAY DIFFRACTIONf_plane_restr0.00611753
X-RAY DIFFRACTIONf_dihedral_angle_d8.21531430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.890.3795950.33291904X-RAY DIFFRACTION58.69
1.89-1.910.42331100.33752107X-RAY DIFFRACTION66.16
1.91-1.940.37661190.31322259X-RAY DIFFRACTION69.86
1.94-1.960.34881300.30692335X-RAY DIFFRACTION73.08
1.96-1.990.37051240.28742435X-RAY DIFFRACTION75.91
1.99-2.020.33521120.27552494X-RAY DIFFRACTION76.29
2.02-2.040.33251340.26782494X-RAY DIFFRACTION78.54
2.04-2.070.35371430.26392665X-RAY DIFFRACTION81.77
2.08-2.110.28821350.24812613X-RAY DIFFRACTION81.96
2.11-2.140.31661490.25262720X-RAY DIFFRACTION84.28
2.14-2.180.30161520.25062795X-RAY DIFFRACTION86.73
2.18-2.220.32371470.22992827X-RAY DIFFRACTION87.39
2.22-2.260.31321540.23313005X-RAY DIFFRACTION92.83
2.26-2.310.29741650.21963071X-RAY DIFFRACTION95.37
2.31-2.360.24581490.223132X-RAY DIFFRACTION97.36
2.36-2.410.28651860.21173226X-RAY DIFFRACTION99.36
2.41-2.470.25841800.20923198X-RAY DIFFRACTION99.38
2.47-2.540.27491860.20793244X-RAY DIFFRACTION99.94
2.54-2.610.25221690.20413199X-RAY DIFFRACTION99.73
2.61-2.70.25731680.19813262X-RAY DIFFRACTION99.85
2.7-2.790.28731560.18923268X-RAY DIFFRACTION99.88
2.79-2.910.24941760.19293251X-RAY DIFFRACTION99.88
2.91-3.040.23511590.19993279X-RAY DIFFRACTION99.91
3.04-3.20.22891400.19073282X-RAY DIFFRACTION99.97
3.2-3.40.2721860.19313270X-RAY DIFFRACTION99.86
3.4-3.660.19051540.1713295X-RAY DIFFRACTION99.88
3.66-4.030.20081880.14973294X-RAY DIFFRACTION99.91
4.03-4.610.17251570.12023334X-RAY DIFFRACTION99.97
4.61-5.80.16341730.13433342X-RAY DIFFRACTION99.91
5.8-29.860.18921940.16073468X-RAY DIFFRACTION98.84

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