PDB-7wdv: Crystal structures of MeBglD2 in complex with various saccharides

ID or keywords:

Entry

Database: PDB / ID: 7wdv

Title

Crystal structures of MeBglD2 in complex with various saccharides

Components

Beta-glucosidase

Keywords

HYDROLASE / glycoside hydrolase family 1

Function / homology

Function and homology information

: / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.812 Å

Authors

Watanabe, M. / Matsuzawa, T. / Nakamichi, Y. / Akita, H. / Yaoi, K.

Funding support

Japan, 1items

Citation

Journal: Appl.Microbiol.Biotechnol. / Year: 2022
Title: Crystal structure of metagenomic beta-glycosidase MeBglD2 in complex with various saccharides
Authors: Matsuzawa, T. / Watanabe, M. / Nakamichi, Y. / Akita, H. / Yaoi, K.

History

Deposition	Dec 22, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7wdv.cif.gz	121 KB	Display	PDBx/mmCIF format
PDB format	pdb7wdv.ent.gz	88.6 KB	Display	PDB format
PDBx/mmJSON format	7wdv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7wdv_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	7wdv_full_validation.pdf.gz	2.4 MB	Display
Data in XML	7wdv_validation.xml.gz	22.4 KB	Display
Data in CIF	7wdv_validation.cif.gz	33.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wd/7wdv ftp://data.pdbj.org/pub/pdb/validation_reports/wd/7wdv	HTTPS FTP

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Related structure data

Related structure data	7wdoC 7wdpC 7wdrC 7wdsC 5xgzS S: Starting model for refinement 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
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Beta-glucosidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	203.051, 203.051, 203.051
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	211
Space group name H-M	I432

Components on special symmetry positions

ID	Model	Components
1	1	A-904- HOH
2	1	A-934- HOH

#1: Protein

Beta-glucosidase

Mass: 52127.074 Da / Num. of mol.: 1 / Mutation: E356A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host:

Escherichia coli (E. coli) / References: UniProt: A0A1E1FFN6, beta-glucosidase

#2: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

#3: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#4: Chemical

ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

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: 3.34 Å³/Da / Density % sol: 63.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl buffer (pH 8.5), 1.2 M lithium sulfate, 0.01 M nickel chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 1.81→50 Å / Num. obs: 64454 / % possible obs: 100 % / Redundancy: 33.6 % / R_merge(I) obs: 0.086 / Net I/σ(I): 77.5
Reflection shell	Resolution: 1.81→1.84 Å / R_merge(I) obs: 0.824 / Num. unique obs: 3170

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0349	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5XGZ

5xgz

Resolution: 1.812→30.002 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.951 / WR_factor R_free: 0.176 / WR_factor R_work: 0.151 / SU B: 1.863 / SU ML: 0.058 / Average fsc free: 0.9753 / Average fsc work: 0.9819 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1848	3209	4.98 %	RANDOM
R_work	0.1581	61232	-	-
all	0.159	-	-	-
obs	-	64441	99.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 18.54 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.812→30.002 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3598	0	55	394	4047

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	3809
X-RAY DIFFRACTION	r_bond_other_d	0.037	0.016	3254
X-RAY DIFFRACTION	r_angle_refined_deg	1.718	1.648	5209
X-RAY DIFFRACTION	r_angle_other_deg	0.998	1.551	7568
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.483	5	452
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.195	10	35
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.052	10	548
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.434	10	202
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	536
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	4452
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	852
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	684
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	2785
X-RAY DIFFRACTION	r_nbtor_refined	0.19	0.2	1867
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1865
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	327
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.141	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.189	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.251	0.2	34
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.165	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.159	1.812	1796
X-RAY DIFFRACTION	r_mcbond_other	2.159	1.812	1796
X-RAY DIFFRACTION	r_mcangle_it	3.231	2.705	2249
X-RAY DIFFRACTION	r_mcangle_other	3.231	2.709	2250
X-RAY DIFFRACTION	r_scbond_it	3.53	2.199	2013
X-RAY DIFFRACTION	r_scbond_other	3.529	2.199	2014
X-RAY DIFFRACTION	r_scangle_it	5.475	3.163	2959
X-RAY DIFFRACTION	r_scangle_other	5.474	3.164	2960
X-RAY DIFFRACTION	r_lrange_it	6.995	23.346	4468
X-RAY DIFFRACTION	r_lrange_other	6.995	23.346	4468

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.812-1.859	0.254	262	0.209	4414	0.211	4676	0.956	0.969	100	0.174
1.859-1.909	0.213	212	0.192	4349	0.193	4561	0.969	0.975	100	0.16
1.909-1.964	0.227	215	0.189	4246	0.191	4461	0.967	0.976	100	0.159
1.964-2.025	0.204	218	0.179	4103	0.18	4321	0.973	0.979	100	0.152
2.025-2.091	0.201	202	0.175	4011	0.176	4213	0.973	0.98	100	0.15
2.091-2.164	0.202	195	0.172	3844	0.173	4039	0.974	0.981	100	0.149
2.164-2.245	0.185	173	0.155	3767	0.157	3940	0.979	0.985	100	0.135
2.245-2.336	0.188	189	0.158	3591	0.16	3780	0.976	0.984	100	0.139
2.336-2.439	0.186	175	0.157	3468	0.158	3643	0.978	0.985	100	0.138
2.439-2.557	0.171	172	0.155	3299	0.155	3471	0.982	0.986	100	0.138
2.557-2.695	0.193	167	0.148	3141	0.15	3308	0.98	0.987	100	0.136
2.695-2.857	0.189	177	0.155	2988	0.157	3165	0.979	0.985	100	0.144
2.857-3.052	0.185	173	0.16	2792	0.162	2965	0.977	0.984	100	0.152
3.052-3.294	0.196	125	0.161	2648	0.163	2773	0.975	0.984	100	0.158
3.294-3.604	0.166	144	0.15	2425	0.151	2569	0.983	0.987	100	0.152
3.604-4.022	0.165	117	0.136	2228	0.138	2345	0.985	0.989	100	0.143
4.022-4.63	0.13	102	0.117	1993	0.118	2095	0.991	0.992	100	0.13
4.63-5.637	0.163	82	0.131	1707	0.133	1789	0.985	0.99	100	0.147
5.637-7.835	0.182	64	0.168	1367	0.169	1431	0.984	0.983	100	0.187
7.835-30.002	0.196	45	0.189	851	0.19	902	0.979	0.977	99.3348	0.231

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