PDB-7quz: Crystal structure of the SeMet octameric C-terminal Big_2-CBM56 d...

ID or keywords:

Entry

Database: PDB / ID: 7quz

Title

Crystal structure of the SeMet octameric C-terminal Big_2-CBM56 domains from Paenibacillus illinoisensis (Bacillus circulans IAM1165) beta-1,3-glucanase H

Components

Beta-1,3-glucanase bglH

Keywords

HYDROLASE / laminarinase / GH16 sub-family 8 / Big_2 / CBM56

Function / homology

Function and homology information

hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function

Biological species

Paenibacillus illinoisensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.156 Å

Authors

Najmudin, S. / Venditto, I. / Fontes, C.M.G.A. / Bule, P.

Funding support

Portugal, European Union, 2items

Citation

Journal: To be published
Title: Structural and biochemical characterization of C-terminal Big_2-CBM56 domains of Bacillus circulans IAM1165 beta-1,3-glucanase H and Paenibacillus sp CBM56
Authors: Najmudin, S. / Venditto, I. / Pires, V.R. / Caseiro, C. / Correia, M.A.S. / Romao, M.J. / Carvalho, A.L. / Fontes, C.M.G.A. / Bule, P.

History

Deposition	Jan 19, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 1, 2023	Provider: repository / Type: Initial release
Revision 2.0	Nov 15, 2023	Group: Atomic model / Author supporting evidence / Data collection Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_audit_support Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_audit_support.country
Revision 2.1	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7quz.cif.gz	956.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7quz_validation.pdf.gz	518.2 KB	Display	wwPDB validaton report
Full document	7quz_full_validation.pdf.gz	534.2 KB	Display
Data in XML	7quz_validation.xml.gz	60.6 KB	Display
Data in CIF	7quz_validation.cif.gz	85.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qu/7quz ftp://data.pdbj.org/pub/pdb/validation_reports/qu/7quz	HTTPS FTP

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Related structure data

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	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (5)

Deposited unit

AAA: Beta-1,3-glucanase bglH

BBB: Beta-1,3-glucanase bglH

CCC: Beta-1,3-glucanase bglH

DDD: Beta-1,3-glucanase bglH

EEE: Beta-1,3-glucanase bglH

FFF: Beta-1,3-glucanase bglH

GGG: Beta-1,3-glucanase bglH

HHH: Beta-1,3-glucanase bglH

hetero molecules

174 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Beta-1,3-glucanase bglH

BBB: Beta-1,3-glucanase bglH

hetero molecules

AAA: Beta-1,3-glucanase bglH

BBB: Beta-1,3-glucanase bglH

hetero molecules

defined by author
Evidence: homology, There are two other crystals forms which also display the tetrameric form.
87.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

CCC: Beta-1,3-glucanase bglH

DDD: Beta-1,3-glucanase bglH

hetero molecules

CCC: Beta-1,3-glucanase bglH

DDD: Beta-1,3-glucanase bglH

hetero molecules

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

3

EEE: Beta-1,3-glucanase bglH

FFF: Beta-1,3-glucanase bglH

GGG: Beta-1,3-glucanase bglH

HHH: Beta-1,3-glucanase bglH

hetero molecules

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

Unit cell

Length a, b, c (Å)	201.125, 51.716, 168.659
Angle α, β, γ (deg.)	90.000, 92.494, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	AAA-413- HOH
2	1	CCC-426- HOH
3	1	CCC-507- HOH
4	1	DDD-505- HOH

#1: Protein	Beta-1,3-glucanase bglH Mass: 21548.229 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: C-terminal Big_2-CBM56 domains / Source: (gene. exp.) Paenibacillus illinoisensis (bacteria) / Gene: bglH, beta-1,3-glucanase / Plasmid: PET-28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: Q45095
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 796 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.56 Å³/Da / Density % sol: 52 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein concentration 30.0 mg/ml, 0.1 M Magnesium Chloride hexahydrate, 0.1 M HEPES pH 7.5, PEG 400 with 30% glycerol added to crystallisation buffer for cryocooling.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 1 / Wavelength: 0.97918 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 2.15→48.772 Å / Num. obs: 94220 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC_1/2: 0.982 / R_merge(I) obs: 0.336 / R_pim(I) all: 0.265 / R_rim(I) all: 0.429 / Net I/σ(I): 4.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
11.8-48.72	4	0.057	649	0.998	0.046	0.074
2.15-2.19	3.6	3.802	4144	0.163	3.161	4.967

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
REFMAC	5.8.0267	refinement
Aimless	0.7.4	data scaling
CRANK2	2.0.25	phasing
MOLREP	2.0.25	phasing
XDS		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 2.156→48.771 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.894 / SU B: 19.895 / SU ML: 0.245 / Cross valid method: FREE R-VALUE / ESU R: 0.274 / ESU R Free: 0.232
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2924	4797	5.093 %
R_work	0.2397	89388	-
all	0.242	-	-
obs	-	94185	99.747 %

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: 26.918 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.99 Å²	-0 Å²	-0.732 Å²
2-	-	-0.491 Å²	-0 Å²
3-	-	-	-0.433 Å²

Refinement step

Cycle: LAST / Resolution: 2.156→48.771 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10726	0	60	796	11582

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	11058
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	10146
X-RAY DIFFRACTION	r_angle_refined_deg	1.766	1.648	15223
X-RAY DIFFRACTION	r_angle_other_deg	1.27	1.571	23356
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.66	5	1479
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.034	26.667	420
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.483	15	1471
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1562
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	13038
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2338
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	1708
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	8840
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	5119
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	5438
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.178	0.2	612
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.044	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.196	0.2	99
X-RAY DIFFRACTION	r_nbd_other	0.253	0.2	245
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.205	0.2	57
X-RAY DIFFRACTION	r_mcbond_it	0.814	1.454	5910
X-RAY DIFFRACTION	r_mcbond_other	0.814	1.453	5909
X-RAY DIFFRACTION	r_mcangle_it	1.465	2.173	7376
X-RAY DIFFRACTION	r_mcangle_other	1.465	2.173	7377
X-RAY DIFFRACTION	r_scbond_it	0.874	1.536	5145
X-RAY DIFFRACTION	r_scbond_other	0.874	1.537	5146
X-RAY DIFFRACTION	r_scangle_it	1.451	2.273	7842
X-RAY DIFFRACTION	r_scangle_other	1.451	2.273	7843
X-RAY DIFFRACTION	r_lrange_it	4.042	17.641	11201
X-RAY DIFFRACTION	r_lrange_other	3.974	17.46	11068

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 (%)
2.156-2.212	0.444	347	0.444	6322	X-RAY DIFFRACTION	97.2016
2.212-2.272	0.406	361	0.393	6387	X-RAY DIFFRACTION	99.9408
2.272-2.338	0.388	324	0.36	6264	X-RAY DIFFRACTION	100
2.338-2.41	0.374	306	0.348	6057	X-RAY DIFFRACTION	99.9372
2.41-2.489	0.391	339	0.336	5859	X-RAY DIFFRACTION	100
2.489-2.577	0.396	287	0.308	5689	X-RAY DIFFRACTION	99.9833
2.577-2.674	0.35	281	0.285	5504	X-RAY DIFFRACTION	100
2.674-2.783	0.31	287	0.246	5269	X-RAY DIFFRACTION	99.964
2.783-2.907	0.303	267	0.231	5113	X-RAY DIFFRACTION	100
2.907-3.049	0.255	254	0.212	4895	X-RAY DIFFRACTION	99.9806
3.049-3.214	0.283	235	0.196	4611	X-RAY DIFFRACTION	100
3.214-3.408	0.263	242	0.194	4379	X-RAY DIFFRACTION	100
3.408-3.644	0.263	202	0.196	4140	X-RAY DIFFRACTION	100
3.644-3.935	0.259	218	0.193	3823	X-RAY DIFFRACTION	100
3.935-4.311	0.231	227	0.161	3565	X-RAY DIFFRACTION	100
4.311-4.819	0.161	180	0.129	3176	X-RAY DIFFRACTION	100
4.819-5.564	0.188	149	0.157	2865	X-RAY DIFFRACTION	99.9337
5.564-6.813	0.268	127	0.168	2445	X-RAY DIFFRACTION	100
6.813-9.627	0.226	115	0.151	1902	X-RAY DIFFRACTION	99.9504
9.627-48.771	0.249	49	0.205	1117	X-RAY DIFFRACTION	98.9813

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.2953	-0.5433	-1.8631	0.5627	0.7844	3.2774	0.0063	-0.1403	0.0868	0.0595	0.0857	-0.1199	-0.0008	0.2308	-0.092	0.1585	-0.0013	0.0783	0.0189	-0.0182	0.0873	9.5447	-25.3583	1.1741
2	0.6711	-0.3102	-1.1816	0.5903	0.732	3.5814	-0.0528	-0.0996	0.0109	0.0717	0.1108	-0.1333	0.2398	0.2596	-0.058	0.176	0.025	0.0647	0.0266	-0.017	0.0761	7.4584	-46.9518	6.21
3	1.1609	0.4334	-1.7789	0.573	-0.7621	3.362	-0.0033	0.1119	0.0626	-0.0753	0.0724	0.1129	0.0309	-0.226	-0.0692	0.151	-0.0018	0.0617	0.0194	0.0118	0.0702	-13.1778	-51.3751	82.6879
4	0.8018	0.287	-1.2761	0.7976	-0.7415	3.4509	-0.0475	0.1353	-0.021	-0.0756	0.0839	0.1715	0.2514	-0.2649	-0.0365	0.2042	-0.026	0.0766	0.0262	-0	0.092	-10.8632	-72.901	77.4537
5	0.6696	-0.3608	-0.8267	0.8294	1.1152	3.6385	-0.017	-0.0708	0.0929	0.0191	0.0999	-0.1138	-0.1592	0.281	-0.083	0.1333	-0.0372	0.0928	0.0644	-0.0083	0.1428	-42.0364	-83.538	41.9557
6	0.6731	0.1091	-0.5294	0.7258	-0.799	3.8764	0.0344	0.1033	-0.0324	-0.0653	0.1394	0.1684	0.2463	-0.2742	-0.1738	0.144	-0.0258	0.0806	0.0717	-0.017	0.1608	-60.4408	-105.0812	39.4412
7	0.8734	0.2378	-1.0282	0.8145	-0.7783	3.683	-0.0061	0.0487	0.0717	-0.0072	0.0922	0.1272	-0.0995	-0.2508	-0.0862	0.1058	0.027	0.0854	0.0384	0.0098	0.1629	-61.1436	-83.5314	44.3837
8	0.6214	0.0094	-0.5075	0.7853	0.9552	4.6732	-0.0184	-0.0712	0.0288	0.111	0.1012	-0.1862	0.2473	0.2459	-0.0828	0.1423	0.0472	0.0722	0.0416	0.0074	0.1664	-42.7708	-104.9927	47.0346

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	24 - 207
2	X-RAY DIFFRACTION	2	ALL	BBB	22 - 207
3	X-RAY DIFFRACTION	3	ALL	CCC	24 - 207
4	X-RAY DIFFRACTION	4	ALL	DDD	21 - 207
5	X-RAY DIFFRACTION	5	ALL	EEE	24 - 207
6	X-RAY DIFFRACTION	6	ALL	FFF	24 - 207
7	X-RAY DIFFRACTION	7	ALL	GGG	24 - 207
8	X-RAY DIFFRACTION	8	ALL	HHH	24 - 207

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