PDB-8b73: Acetivibrio clariflavus beta-1,4-xylanase of Glycoside Hydrolase ...

ID or keywords:

Entry

Database: PDB / ID: 8b73

Title

Acetivibrio clariflavus beta-1,4-xylanase of Glycoside Hydrolase Family 10 (AcXyn10A).

Components

Beta-xylanase

Keywords

HYDROLASE / Beta-1 / 4-xylanase / Glycosyl hydrolases / Acetivibrio clariflavus

Function / homology

Function and homology information

endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function

Biological species

Acetivibrio clariflavus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.24 Å

Authors

Hussain, N. / James, J.H. / Halina, M.

Funding support

United Kingdom, 2items

Citation

Journal: To Be Published
Title: To be decided. Not published yet.
Authors: Hussain, N. / James, J.H. / Halina, M.

History

Deposition	Sep 28, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 19, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2022	Group: Database references / Category: struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code ..._struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
Revision 1.2	Apr 26, 2023	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3	Jun 19, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8b73.cif.gz	436.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8b73_validation.pdf.gz	424.2 KB	Display	wwPDB validaton report
Full document	8b73_full_validation.pdf.gz	427.4 KB	Display
Data in XML	8b73_validation.xml.gz	28.6 KB	Display
Data in CIF	8b73_validation.cif.gz	40.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b7/8b73 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/8b73	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	#217 - Jan 2018 Opioid Receptors similarity (1)

Deposited unit

A: Beta-xylanase

B: Beta-xylanase

95.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	80.566, 88.916, 173.479
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 9 - 413 / Label seq-ID: 9 - 413

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Beta-xylanase Mass: 47527.777 Da / Num. of mol.: 2 / Mutation: 1-2insG Source method: isolated from a genetically manipulated source Details: Acetivibrio clariflavus beta-1,4-xylanase of Glycoside Hydrolase Family 10 Source: (gene. exp.) Acetivibrio clariflavus (bacteria) / Strain: DSM 19732 / NBRC 101661 / EBR45 / Gene: Clocl_0045 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: G8LZE0, endo-1,4-beta-xylanase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Beta-xylanase

Mass: 47527.777 Da / Num. of mol.: 2 / Mutation: 1-2insG
Source method: isolated from a genetically manipulated source
Details: Acetivibrio clariflavus beta-1,4-xylanase of Glycoside Hydrolase Family 10
Source: (gene. exp.)

Acetivibrio clariflavus (bacteria) / Strain: DSM 19732 / NBRC 101661 / EBR45 / Gene: Clocl_0045
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: G8LZE0, endo-1,4-beta-xylanase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.27243114 Å³/Da / Density % sol: 62.436615 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: H6 conditions of JCSG+ HTS 0.1 M Ammonium acetate 0.1 M BIS-Tris, 17 % w/v PEG 10,000 109.79mM Xyltetraose (10X) with AcXynA protein in buffer containing 50mM NaCl, 20mM Tris-Cl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 7, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.24→89.58 Å / Num. obs: 61326 / % possible obs: 99.81 % / Redundancy: 12.7 % / B_iso Wilson estimate: 46.76 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.166 / R_pim(I) all: 0.05 / R_rim(I) all: 0.173 / Net I/σ(I): 8
Reflection shell	Resolution: 2.24→2.29 Å / Redundancy: 13.5 % / R_merge(I) obs: 2.685 / Num. unique obs: 3029 / CC_1/2: 0.405 / R_pim(I) all: 0.764 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
xia2		data reduction
xia2.multiplex		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.24→62.089 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.94 / SU B: 14.841 / SU ML: 0.163 / Cross valid method: FREE R-VALUE / ESU R: 0.222 / ESU R Free: 0.181
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2316	3049	5.053 %
R_work	0.206	57290	-
all	0.207	-	-
obs	-	60339	99.376 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 52.222 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.412 Å²	0 Å²	-0 Å²
2-	-	-0.407 Å²	0 Å²
3-	-	-	0.819 Å²

Refinement step

Cycle: LAST / Resolution: 2.24→62.089 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6578	0	0	151	6729

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	6772
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6100
X-RAY DIFFRACTION	r_angle_refined_deg	0.95	1.648	9188
X-RAY DIFFRACTION	r_angle_other_deg	0.341	1.569	14264
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.278	5	812
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.448	5	24
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.934	10	1176
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.832	10	326
X-RAY DIFFRACTION	r_chiral_restr	0.049	0.2	990
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	7570
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1366
X-RAY DIFFRACTION	r_nbd_refined	0.192	0.2	1215
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	5575
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	3274
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	3521
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	183
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.005	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.196	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.209	0.2	34
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.228	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	0.674	3.28	3248
X-RAY DIFFRACTION	r_mcbond_other	0.674	3.28	3248
X-RAY DIFFRACTION	r_mcangle_it	1.174	4.919	4060
X-RAY DIFFRACTION	r_mcangle_other	1.174	4.919	4061
X-RAY DIFFRACTION	r_scbond_it	0.706	3.334	3524
X-RAY DIFFRACTION	r_scbond_other	0.706	3.334	3525
X-RAY DIFFRACTION	r_scangle_it	1.196	4.974	5128
X-RAY DIFFRACTION	r_scangle_other	1.195	4.974	5129
X-RAY DIFFRACTION	r_lrange_it	2.386	38.291	7455
X-RAY DIFFRACTION	r_lrange_other	2.38	38.231	7439
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.04	0.05	14006

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.04045	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.04045	0.0501

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
2.24-2.298	0.354	196	0.359	3922	0.359	4433	0.892	0.891	92.8942	0.357
2.298-2.361	0.356	215	0.351	4049	0.351	4296	0.916	0.907	99.2551	0.347
2.361-2.429	0.339	228	0.318	3947	0.319	4175	0.924	0.929	100	0.31
2.429-2.504	0.298	218	0.291	3887	0.292	4105	0.946	0.945	100	0.282
2.504-2.586	0.286	189	0.271	3761	0.272	3951	0.949	0.956	99.9747	0.255
2.586-2.677	0.276	235	0.25	3600	0.251	3841	0.951	0.965	99.8438	0.225
2.677-2.777	0.26	195	0.237	3524	0.238	3720	0.961	0.968	99.9731	0.205
2.777-2.891	0.311	144	0.236	3402	0.239	3555	0.944	0.967	99.7468	0.206
2.891-3.019	0.296	157	0.238	3260	0.24	3422	0.942	0.966	99.8539	0.205
3.019-3.166	0.246	166	0.226	3121	0.227	3287	0.96	0.968	100	0.197
3.166-3.337	0.247	150	0.223	2997	0.225	3149	0.965	0.971	99.9365	0.201
3.337-3.538	0.245	151	0.225	2821	0.226	2973	0.965	0.97	99.9664	0.204
3.538-3.782	0.234	137	0.194	2632	0.195	2770	0.974	0.981	99.9639	0.177
3.782-4.083	0.193	139	0.17	2496	0.171	2636	0.981	0.984	99.9621	0.156
4.083-4.471	0.159	127	0.149	2285	0.149	2412	0.986	0.988	100	0.14
4.471-4.996	0.169	100	0.145	2097	0.146	2197	0.984	0.988	100	0.135
4.996-5.762	0.158	104	0.157	1868	0.157	1972	0.986	0.988	100	0.147
5.762-7.042	0.221	88	0.186	1579	0.188	1667	0.981	0.983	100	0.172
7.042-9.896	0.188	66	0.148	1272	0.15	1338	0.985	0.987	100	0.148
9.896-62.089	0.287	44	0.226	755	0.229	799	0.939	0.952	100	0.209

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	5.6128	3.176	4.9913	2.0849	2.7121	5.8682	0.1867	-0.1818	0.2052	-0.1281	-0.1853	0.2845	0.2113	-0.3354	-0.0014	0.3155	0.0082	-0.0702	0.3102	-0.0246	0.15	17.61	21.695	99.081
2	1.7098	0.8034	-0.3787	2.0098	-0.1274	1.1703	0.0211	-0.1047	-0.3336	-0.0006	-0.1329	-0.4902	0.2109	0.0967	0.1118	0.2195	0.018	0.0239	0.155	0.0342	0.1664	49.906	26.239	112.722
3	2.5469	0.1365	3.1986	1.2761	0.1698	6.0929	0.2116	-0.1462	-0.2555	-0.086	-0.163	0.1521	0.3259	-0.3196	-0.0486	0.2203	-0.0557	0.015	0.1931	-0.0111	0.1401	24.831	20.523	111.992
4	16.6275	11.4328	4.5987	8.2383	4.6271	7.041	0.0544	0.4135	-1.2184	0.0272	0.3089	-0.8841	-0.0638	0.125	-0.3633	0.3318	0.039	-0.1311	0.1846	-0.066	0.3995	22.037	23.1	92.462
5	5.7745	3.5961	-5.7377	2.4521	-3.0579	7.0347	0.0579	-0.2754	-0.276	-0.0073	-0.2138	-0.2291	-0.0789	0.2789	0.1559	0.1716	0.0193	0.0074	0.299	0.0254	0.1186	95.562	68.433	100.363
6	1.7606	0.2325	0.1635	1.1742	0.133	1.5465	-0.0456	-0.0608	0.0953	-0.0353	-0.0126	0.11	-0.1753	0.0406	0.0583	0.1524	0.0185	0.0189	0.152	0.006	0.0523	62.719	65.878	111.225
7	3.3539	-0.5122	-2.8593	0.7493	-0.0828	4.2138	0.1415	-0.3886	0.1655	-0.0521	-0.1169	-0.1726	-0.2398	0.5766	-0.0246	0.1899	-0.0815	-0.0131	0.3028	-0.0128	0.1394	87.581	71.374	113.279
8	9.3972	0.6634	-2.1317	0.2434	-1.5717	11.2597	-0.0444	0.0024	-0.3673	-0.0968	0.0628	0.0257	0.4383	-0.0954	-0.0184	0.3634	-0.0096	-0.0556	0.3485	0.0924	0.2988	91.904	68.037	95.366

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	9 - 41
2	X-RAY DIFFRACTION	2	ALL	A	42 - 337
3	X-RAY DIFFRACTION	3	ALL	A	338 - 402
4	X-RAY DIFFRACTION	4	ALL	A	403 - 413
5	X-RAY DIFFRACTION	5	ALL	B	9 - 41
6	X-RAY DIFFRACTION	6	ALL	B	42 - 337
7	X-RAY DIFFRACTION	7	ALL	B	338 - 402
8	X-RAY DIFFRACTION	8	ALL	B	403 - 413

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