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

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Basic information

Entry
Database: PDB / ID: 8zlg
TitleCrystal structure of a beta-1,4-endoglucanase from Bispora sp. MEY-1
ComponentsEndo-beta-1, 4-glucanase
KeywordsHYDROLASE / Promiscuous cellulase
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 / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZheng, J. / Luo, H.
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.
History
DepositionMay 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 2.0Jun 4, 2025Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-1, 4-glucanase
B: Endo-beta-1, 4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1418
Polymers70,8142
Non-polymers1,3276
Water7,242402
1
A: Endo-beta-1, 4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0714
Polymers35,4071
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-beta-1, 4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0714
Polymers35,4071
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.101, 115.101, 107.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSLEULEUAA8 - 3198 - 319
d_12NAGNAGNAGNAGAC401
d_13NAGNAGNAGNAGAD402
d_14NAGNAGNAGNAGAE403
d_21LYSLYSLEULEUBB8 - 3198 - 319
d_22NAGNAGNAGNAGBF401
d_23NAGNAGNAGNAGBG402
d_24NAGNAGNAGNAGBH403

NCS oper: (Code: givenMatrix: (0.250197483141, 0.968157385316, 0.00851449872836), (0.968194251885, -0.250178090109, -0.00328844140322), (-0.0010535878006, 0.00906644848903, -0.999958343865)Vector: 49. ...NCS oper: (Code: given
Matrix: (0.250197483141, 0.968157385316, 0.00851449872836), (0.968194251885, -0.250178090109, -0.00328844140322), (-0.0010535878006, 0.00906644848903, -0.999958343865)
Vector: 49.6591944154, -63.7187408592, -67.9063750851)

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Components

#1: Protein Endo-beta-1, 4-glucanase


Mass: 35406.906 Da / Num. of mol.: 2
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) / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A150VE32, cellulase
#2: 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.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 291 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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 26711 / % possible obs: 80 % / Redundancy: 3.1 % / CC1/2: 0.961 / CC star: 0.99 / Rpim(I) all: 0.073 / Rrim(I) all: 0.147 / Net I/σ(I): 10.6
Reflection shellResolution: 2.34→6.1 Å / Num. unique obs: 16508 / CC1/2: 0.961 / Rpim(I) all: 0.073

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→46.44 Å / SU ML: 0.2823 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7493
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 1272 4.76 %
Rwork0.1833 25439 -
obs0.1865 26711 80.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.8 Å2
Refinement stepCycle: LAST / Resolution: 2.25→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 84 402 5302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785020
X-RAY DIFFRACTIONf_angle_d0.97246846
X-RAY DIFFRACTIONf_chiral_restr0.0576746
X-RAY DIFFRACTIONf_plane_restr0.0072886
X-RAY DIFFRACTIONf_dihedral_angle_d6.6333712
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.98496125117 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.340.31831450.21152876X-RAY DIFFRACTION82.65
2.34-2.450.29331170.20922863X-RAY DIFFRACTION81.71
2.45-2.580.34091270.25182673X-RAY DIFFRACTION76.11
2.58-2.740.28181270.23252456X-RAY DIFFRACTION70.46
2.74-2.950.40131180.23942322X-RAY DIFFRACTION66.56
2.95-3.250.29831100.21042353X-RAY DIFFRACTION66.73
3.25-3.720.22591530.1582958X-RAY DIFFRACTION84.81
3.72-4.690.18251850.14313420X-RAY DIFFRACTION98.07
4.69-46.440.2081900.16823518X-RAY DIFFRACTION98.96

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