PDB-9bwh: Crystal structure of cellulose oxidative enzyme with glycerol

ID or keywords:

Entry

Database: PDB / ID: 9bwh

Title

Crystal structure of cellulose oxidative enzyme with glycerol

Components

Cellulose oxidative enzyme

Keywords

OXIDOREDUCTASE / Carbohydrate oxidase / copper complex

Function / homology

COPPER (II) ION

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Morais, M.A.B. / Santos, C.A. / Araujo, E.A. / Santos, C.R. / Morao, L.G. / Motta, M.L. / Murakami, M.T.

Funding support

Brazil, 1items

Citation

Journal: Nature / Year: 2025
Title: A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion.
Authors: Santos, C.A. / Morais, M.A.B. / Mandelli, F. / Lima, E.A. / Miyamoto, R.Y. / Higasi, P.M.R. / Araujo, E.A. / Paixao, D.A.A. / Junior, J.M. / Motta, M.L. / Streit, R.S.A. / Morao, L.G. / ...

History

Deposition	May 21, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 4, 2024	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Feb 26, 2025	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Apr 2, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9bwh.cif.gz	115.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9bwh.ent.gz	88 KB	Display	PDB format
PDBx/mmJSON format	9bwh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bw/9bwh ftp://data.pdbj.org/pub/pdb/validation_reports/bw/9bwh	HTTPS FTP

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Related structure data

Related structure data	9bwfC 9bwiC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cellulose oxidative enzyme

B: Cellulose oxidative enzyme

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	72.689, 72.689, 98.739
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-384- HOH
2	1	A-400- HOH

#1: Protein	Cellulose oxidative enzyme Mass: 15772.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.47 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: Trisodium citrate, HEPES buffer pH 7.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.977 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 29, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.977 Å / Relative weight: 1

Reflection

Resolution: 1.65→38.85 Å / Num. obs: 36854 / % possible obs: 95.3 % / Redundancy: 19.9 % / CC_1/2: 0.985 / R_merge(I) obs: 0.207 / R_rim(I) all: 0.264 / Net I/σ(I): 2.77

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.65-1.75	5.349	5497	0.018	6.853	1
1.75-1.87	2.626	5310	0.073	3.329	1
1.87-2.02	1.297	4965	0.285	1.645	1
2.02-2.21	0.674	4571	0.547	0.863	1
2.21-2.47	0.456	4168	0.709	0.585	1
2.47-2.85	0.288	3754	0.888	0.365	1
2.85-3.49	0.133	3125	0.969	0.17	1
3.49-4.92	0.068	2383	0.99	0.087	1

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→38.85 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1859	1841	5 %
R_work	0.1708	-	-
obs	0.1715	36830	99.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→38.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1874	0	14	201	2089

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	1938
X-RAY DIFFRACTION	f_angle_d	1.479	2630
X-RAY DIFFRACTION	f_dihedral_angle_d	14.538	720
X-RAY DIFFRACTION	f_chiral_restr	0.102	296
X-RAY DIFFRACTION	f_plane_restr	0.01	328

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 (%)
1.65-1.69	0.3118	136	0.3011	2606	X-RAY DIFFRACTION	99
1.69-1.74	0.2968	140	0.2769	2653	X-RAY DIFFRACTION	100
1.74-1.8	0.3058	141	0.2915	2679	X-RAY DIFFRACTION	100
1.8-1.87	0.276	140	0.2343	2662	X-RAY DIFFRACTION	100
1.87-1.94	0.2275	139	0.1997	2644	X-RAY DIFFRACTION	100
1.94-2.03	0.2099	141	0.1652	2677	X-RAY DIFFRACTION	100
2.03-2.14	0.1875	141	0.1681	2688	X-RAY DIFFRACTION	100
2.14-2.27	0.1905	140	0.1754	2658	X-RAY DIFFRACTION	100
2.27-2.44	0.1718	141	0.1666	2682	X-RAY DIFFRACTION	100
2.44-2.69	0.1965	143	0.1786	2716	X-RAY DIFFRACTION	100
2.69-3.08	0.2103	143	0.1661	2712	X-RAY DIFFRACTION	100
3.08-3.88	0.148	144	0.1493	2737	X-RAY DIFFRACTION	100
3.88-38.85	0.1548	152	0.148	2875	X-RAY DIFFRACTION	100

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	1.6435	-0.5312	0.0127	1.1821	0.0368	1.6604	0.0087	0.012	0.0739	-0.0423	-0.0012	-0.234	-0.0336	0.1719	-0.0077	0.2136	0.0211	0.0101	0.2153	0.0249	0.227	50.8519	-16.8707	-10.9014
2	6.064	5.7985	-5.7593	5.6328	-5.4408	5.525	0.5397	0.3679	1.3839	1.0175	0.2017	0.5828	-1.3027	-0.577	-0.6241	0.5374	0.026	-0.0399	0.3344	0.0339	0.4979	49.0161	-1.2738	-2.5283
3	1.3897	0.1831	0.4459	2.0313	-0.739	3.4617	-0.0187	-0.0251	0.1957	0.0532	-0.0303	-0.3067	-0.17	0.1627	0.0506	0.21	0.0282	-0.0119	0.1894	0.0129	0.2459	49.9995	-9.0201	-8.1925
4	8.2206	-8.5576	6.6029	9.5089	-7.2365	6.5873	0.3246	0.676	0.3203	-0.2273	-0.4488	-0.4035	-0.0988	0.5268	0.1885	0.2565	0.044	0.0737	0.2473	0.0287	0.2321	54.2767	-17.6359	-20.9587
5	4.0362	4.4028	-3.3824	4.863	-3.5924	3.0397	0.0926	0.3326	-0.6407	0.1467	-0.0796	0.149	-0.013	-0.1444	0.0115	0.2942	0.0493	-0.0049	0.228	-0.0138	0.3041	48.6691	-30.5425	-17.5053
6	9.0637	6.5379	-0.5829	8.1243	-3.356	5.8772	0.0064	-0.5049	0.1415	0.3363	-0.1497	-0.0679	-0.2308	-0.2737	0.0777	0.3089	0.123	0.0085	0.2059	-0.0464	0.2306	36.5787	-5.2019	-4.4897
7	7.4396	4.3287	1.9587	7.2691	3.3382	2.2499	0.407	0.4385	0.5414	-0.6818	-0.5918	0.4742	-0.9033	-0.617	0.1138	0.2965	0.0629	0.0131	0.3912	0.0579	0.4141	21.6787	-13.7987	-10.7097
8	9.6592	6.7908	-0.1059	4.7863	0.0434	5.5792	0.2343	-0.4131	0.0954	0.4765	-0.1555	0.3506	-0.0578	-0.5594	-0.1588	0.215	0.069	0.0166	0.2495	0.0368	0.2239	31.7184	-9.0922	-10.3785
9	4.281	4.0377	-3.9125	5.1192	-2.4414	4.9704	0.0437	0.0065	0.1824	-0.1075	0.0736	0.1601	0.0643	-0.155	0.0051	0.2015	0.0426	0.0045	0.2256	0.0436	0.224	35.7859	-11.0852	-13.6609
10	1.1146	0.7044	-2.0813	0.3444	-1.2172	3.9587	-0.0953	0.019	-0.1175	-0.1505	0.051	0.1164	0.1795	-0.201	0.0549	0.3067	0.0187	0.0018	0.301	0.0259	0.249	26.134	-20.1026	-17.8187
11	3.163	0.651	1.9839	1.7909	0.1303	7.2154	0.19	-0.0507	-0.1058	-0.0882	-0.0244	0.0825	0.3251	-0.155	-0.1608	0.1934	0.0303	0.0015	0.136	0.0308	0.1769	34.5924	-24.0651	-13.5733
12	8.0907	1.0401	5.6883	9.7776	1.722	4.0883	0.2926	0.3737	-0.3548	-0.5285	-0.198	0.0688	0.8953	0.1481	0.0342	0.3209	0.0082	-0.0056	0.2198	0.0357	0.2972	33.5735	-31.3633	-17.4433
13	6.054	-5.7728	5.9082	5.7194	-5.6453	5.6083	0.1192	0.1605	-0.0392	-0.302	-0.1755	-0.0409	0.1585	0.0663	0.008	0.2536	-0.0126	0.0029	0.1629	-0.0036	0.185	36.2299	-22.2524	-20.5564
14	6.7082	2.3427	-3.0747	6.4423	-3.4443	2.4695	0.0929	-0.0898	-0.1613	0.0229	0.1453	0.3122	0.2325	-0.7511	-0.2715	0.1994	-0.0269	-0.015	0.23	0.06	0.2229	26.9031	-26.4708	-11.717
15	3.8894	4.8687	-4.3655	7.4032	-6.2922	5.2468	0.0467	0.1613	-0.0204	-0.0083	0.075	0.0453	-0.2054	-0.398	-0.2133	0.2237	0.0342	0.0177	0.223	0.0197	0.1955	35.3663	-16.2334	-13.2149
16	8.4281	-6.459	-6.4975	6.2434	7.3036	9.3208	0.0467	0.3022	0.1961	-0.1077	-0.0106	0.228	-0.002	-0.3965	-0.0128	0.2395	0.0161	-0.0112	0.1807	0.0354	0.2032	30.6677	-6.2284	-18.5908
17	9.7583	-2.6118	4.6797	9.0263	3.3688	8.6296	-0.451	-0.3752	0.1216	0.4507	0.5165	-0.5653	-0.1642	-0.2009	-0.0224	0.4388	0.0609	-0.0285	0.3022	-0.0141	0.2577	33.9925	-0.387	-5.0464

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 63 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 64 through 71 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 72 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 through 108 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 109 through 115 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid -1 through 10 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 11 through 16 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 17 through 24 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 25 through 35 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 36 through 48 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 49 through 63 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 64 through 71 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 72 through 83 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 84 through 91 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 92 through 99 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 100 through 108 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 109 through 115 )

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