PDB-8zi5: Crystal structure of a beta-1,4-endoglucanase from Bispora sp. ME...

ID or keywords:

Entry

Database: PDB / ID: 8zi5

Title

Crystal structure of a beta-1,4-endoglucanase from Bispora sp. MEY-1 in complex with mannotetrose

Components

cellulase

Keywords

HYDROLASE / Promiscuous cellulase in complex with sugars

Function / homology

glucan catabolic process / cellulase / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / DI(HYDROXYETHYL)ETHER / cellulase

Function and homology information

Biological species

Bispora sp. MEY-1 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Zheng, J. / Luo, H.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Unraveling the Key Determinants of Substrate Promiscuity in Glycoside Hydrolase Family 5_5 Cellulases
Authors: Zheng, J. / Zheng, F. / Hanqing, L. / Xiao, W. / Xing, Q. / Xiaolu, W. / Huoqing, H. / Bin, Y. / Jian, T. / Huiying, L.

History

Deposition	May 13, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	May 21, 2025	Provider: repository / Type: Initial release
Revision 2.0	May 28, 2025	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_validate_close_contact 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 / _pdbx_validate_close_contact.auth_seq_id_1

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8zi5.cif.gz	296.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8zi5_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8zi5_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8zi5_validation.xml.gz	76 KB	Display
Data in CIF	8zi5_validation.cif.gz	107 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zi/8zi5 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/8zi5	HTTPS FTP

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Related structure data

Related structure data	8zikC 8zlgC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: cellulase

B: cellulase

C: cellulase

D: cellulase

hetero molecules

148 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: cellulase

hetero molecules

defined by author
Evidence: gel filtration
37.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: cellulase

hetero molecules

defined by author
37 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: cellulase

hetero molecules

defined by author
37.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: cellulase

hetero molecules

defined by author
36.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.721, 88.593, 175.743
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁
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

#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-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose

Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 3 / Source method: obtained synthetically

Descriptor	Type	Program
DManpb1-4DManpb1-4DManpb1-4DManpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,4,3/[a1122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1	WURCS	PDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}	LINUCS	PDB-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.: 18
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#4: Chemical

ChemComp-PEG / DI(HYDROXYETHYL)ETHER

Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1691 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.92 Å³/Da / Density % sol: 35.79 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U / Wavelength: 0.979183 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979183 Å / Relative weight: 1

Reflection

Resolution: 1.73→18.51 Å / Num. obs: 110885 / % possible obs: 97.6 % / Redundancy: 10.5 % / CC_1/2: 0.964 / CC star: 0.991 / R_merge(I) obs: 0.117 / R_pim(I) all: 0.039 / R_rim(I) all: 0.123 / Χ²: 2.021 / Net I/σ(I): 6.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.73-1.76	8.7	0.403	5590	0.917	0.978	0.144	0.429	0.456	100
1.76-1.79	9.2	0.368	5621	0.93	0.982	0.128	0.391	0.494	100
1.79-1.83	9.7	0.333	5591	0.942	0.985	0.112	0.352	0.57	99.9
1.83-1.86	10.3	0.31	5601	0.958	0.989	0.101	0.327	0.617	99.9
1.86-1.9	11	0.281	5621	0.962	0.99	0.088	0.294	0.71	99.9
1.9-1.95	12.2	0.278	5649	0.972	0.993	0.082	0.29	0.808	99.8
1.95-2	12.1	0.229	5595	0.969	0.992	0.068	0.239	0.973	99.9
2-2.05	11.8	0.212	5641	0.975	0.994	0.065	0.222	1.115	99.8
2.05-2.11	11.1	0.189	5635	0.976	0.994	0.06	0.199	1.256	99.6
2.11-2.18	11.2	0.168	5588	0.982	0.995	0.053	0.177	1.218	99.6
2.18-2.26	11.5	0.159	5612	0.981	0.995	0.049	0.167	1.463	99.3
2.26-2.35	11.2	0.146	5601	0.981	0.995	0.046	0.153	1.629	99
2.35-2.45	10.6	0.13	5644	0.975	0.994	0.043	0.137	1.768	99.2
2.45-2.58	11.1	0.115	5604	0.983	0.996	0.037	0.121	1.844	99
2.58-2.75	11	0.105	5584	0.979	0.995	0.034	0.11	2.136	98.1
2.75-2.96	10.3	0.092	5523	0.973	0.993	0.031	0.098	2.21	97.1
2.96-3.26	9.9	0.081	5403	0.97	0.992	0.028	0.086	3.2	94.1
3.26-3.73	8.7	0.074	5104	0.973	0.993	0.028	0.079	4.862	88.6
3.73-4.69	8.2	0.063	4947	0.964	0.991	0.025	0.069	7.043	84.9
4.69-50	9.3	0.064	5731	0.969	0.992	0.025	0.069	9.474	94.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.1_4122: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.73→18.51 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1967	5603	5.07 %
R_work	0.1509	-	-
obs	0.1531	110537	97.26 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.73→18.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9701	0	223	1691	11615

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10173
X-RAY DIFFRACTION	f_angle_d	0.994	13896
X-RAY DIFFRACTION	f_dihedral_angle_d	7.582	1453
X-RAY DIFFRACTION	f_chiral_restr	0.06	1566
X-RAY DIFFRACTION	f_plane_restr	0.007	1762

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.73-1.75	0.1989	171	0.1472	3347	X-RAY DIFFRACTION	94
1.75-1.77	0.238	204	0.1539	3552	X-RAY DIFFRACTION	100
1.77-1.79	0.2049	193	0.1513	3547	X-RAY DIFFRACTION	100
1.79-1.82	0.1897	220	0.1474	3544	X-RAY DIFFRACTION	100
1.82-1.84	0.2084	196	0.1531	3543	X-RAY DIFFRACTION	100
1.84-1.87	0.2174	205	0.1558	3507	X-RAY DIFFRACTION	100
1.87-1.89	0.2154	199	0.1539	3569	X-RAY DIFFRACTION	100
1.89-1.92	0.2084	190	0.1487	3552	X-RAY DIFFRACTION	100
1.92-1.95	0.2236	178	0.1446	3585	X-RAY DIFFRACTION	100
1.95-1.98	0.1618	195	0.138	3537	X-RAY DIFFRACTION	100
1.98-2.02	0.1934	197	0.143	3556	X-RAY DIFFRACTION	100
2.02-2.05	0.2118	175	0.1476	3595	X-RAY DIFFRACTION	100
2.05-2.09	0.1956	183	0.1426	3541	X-RAY DIFFRACTION	100
2.09-2.14	0.1802	170	0.1421	3570	X-RAY DIFFRACTION	100
2.14-2.18	0.2131	158	0.1442	3602	X-RAY DIFFRACTION	100
2.18-2.23	0.1936	198	0.1464	3533	X-RAY DIFFRACTION	99
2.23-2.29	0.2226	182	0.1504	3553	X-RAY DIFFRACTION	99
2.29-2.35	0.2188	182	0.1482	3563	X-RAY DIFFRACTION	99
2.35-2.42	0.2051	178	0.1527	3551	X-RAY DIFFRACTION	99
2.42-2.5	0.1981	200	0.1534	3580	X-RAY DIFFRACTION	99
2.5-2.59	0.2208	188	0.1519	3551	X-RAY DIFFRACTION	99
2.59-2.69	0.1832	199	0.154	3526	X-RAY DIFFRACTION	98
2.69-2.81	0.1854	195	0.1525	3496	X-RAY DIFFRACTION	97
2.81-2.96	0.1907	192	0.1493	3503	X-RAY DIFFRACTION	97
2.96-3.14	0.2216	191	0.1538	3430	X-RAY DIFFRACTION	95
3.14-3.38	0.1927	181	0.154	3306	X-RAY DIFFRACTION	91
3.38-3.72	0.1994	163	0.1523	3191	X-RAY DIFFRACTION	87
3.72-4.26	0.1667	174	0.141	3112	X-RAY DIFFRACTION	85
4.26-5.34	0.1626	159	0.1425	3201	X-RAY DIFFRACTION	86
5.34-18.51	0.1997	187	0.1791	3691	X-RAY DIFFRACTION	96

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