PDB-9dr6: Crystal structure of Catechol 1,2-dioxygenase from Burkholderia m...

ID or keywords:

Entry

Database: PDB / ID: 9dr6

Title

Crystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Zinc bound)

Components

Catechol 1,2-dioxygenase

Keywords

HYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Catechol 1 / 2-dioxygenase

Function / homology

Function and homology information

catechol-containing compound catabolic process / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / beta-ketoadipate pathway / ferric iron binding
Similarity search - Function

Biological species

Burkholderia multivorans ATCC 17616 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Zinc bound)
Authors: Liu, L. / Enayati, P. / Lovell, S. / Buchko, G.W. / Battaile, K.P.

History

Deposition	Sep 25, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 2, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dr6.cif.gz	281.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9dr6.ent.gz	224.9 KB	Display	PDB format
PDBx/mmJSON format	9dr6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dr6_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	9dr6_full_validation.pdf.gz	1.9 MB	Display
Data in XML	9dr6_validation.xml.gz	38.8 KB	Display
Data in CIF	9dr6_validation.cif.gz	56.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dr/9dr6 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/9dr6	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

Deposited unit

A: Catechol 1,2-dioxygenase

B: Catechol 1,2-dioxygenase

hetero molecules

70.5 kDa, 2 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)	115.247, 52.271, 120.634
Angle α, β, γ (deg.)	90.00, 92.50, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 2 molecules AB

#1: Protein	Catechol 1,2-dioxygenase / BumuA.00117.a.B1 Mass: 34518.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia multivorans ATCC 17616 (bacteria) Gene: catA / Plasmid: BumuA.00117.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KXJ8, catechol 1,2-dioxygenase

#1: Protein

Catechol 1,2-dioxygenase / BumuA.00117.a.B1

Mass: 34518.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia multivorans ATCC 17616 (bacteria)
Gene: catA / Plasmid: BumuA.00117.a.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KXJ8, catechol 1,2-dioxygenase

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Non-polymers , 6 types, 892 molecules

#2: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₄H₅₀O₁₃ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 879 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.63 Å³/Da / Density % sol: 53.22 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% (w/v) 4000, 0.2M CaCl2, 0.1M Tris 8.5, BumuA.00107.d.A2.PW32075 at 21.7 mg/mL. plate Liu-S-128 B7. Protein prepared in the presence of ZnCl2. Puck: PSL-1603, Cryo: 32% (w/v) 4000, 0.2M CaCl2, 0.1M Tris 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 14, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.75→120.52 Å / Num. obs: 72503 / % possible obs: 99.8 % / Redundancy: 4.1 % / CC_1/2: 0.996 / R_merge(I) obs: 0.107 / R_pim(I) all: 0.058 / R_rim(I) all: 0.122 / Χ²: 0.96 / Net I/σ(I): 8.4 / Num. measured all: 300709
Reflection shell	Resolution: 1.75→1.8 Å / % possible obs: 99.9 % / Redundancy: 4 % / R_merge(I) obs: 0.887 / Num. measured all: 21182 / Num. unique obs: 5311 / CC_1/2: 0.715 / R_pim(I) all: 0.495 / R_rim(I) all: 1.019 / Χ²: 0.98 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5449: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→60.26 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.192	3582	4.94 %
R_work	0.1525	-	-
obs	0.1545	72471	99.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.75→60.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4687	0	76	879	5642

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5078
X-RAY DIFFRACTION	f_angle_d	0.793	6915
X-RAY DIFFRACTION	f_dihedral_angle_d	12.608	1921
X-RAY DIFFRACTION	f_chiral_restr	0.049	752
X-RAY DIFFRACTION	f_plane_restr	0.008	926

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 (%)
1.75-1.77	0.3155	140	0.2477	2578	X-RAY DIFFRACTION	100
1.77-1.8	0.2774	133	0.2351	2683	X-RAY DIFFRACTION	100
1.8-1.82	0.2629	148	0.2185	2591	X-RAY DIFFRACTION	100
1.82-1.85	0.2803	123	0.2117	2645	X-RAY DIFFRACTION	100
1.85-1.88	0.2619	138	0.2042	2636	X-RAY DIFFRACTION	100
1.88-1.91	0.2363	149	0.2025	2621	X-RAY DIFFRACTION	99
1.91-1.94	0.222	131	0.1971	2640	X-RAY DIFFRACTION	99
1.94-1.98	0.2269	158	0.1753	2633	X-RAY DIFFRACTION	100
1.98-2.02	0.2284	145	0.1727	2614	X-RAY DIFFRACTION	100
2.02-2.06	0.2264	117	0.1607	2640	X-RAY DIFFRACTION	100
2.06-2.1	0.2091	143	0.154	2658	X-RAY DIFFRACTION	100
2.1-2.15	0.1775	129	0.1484	2635	X-RAY DIFFRACTION	100
2.15-2.2	0.1942	130	0.1441	2636	X-RAY DIFFRACTION	100
2.2-2.26	0.228	116	0.1463	2724	X-RAY DIFFRACTION	100
2.26-2.33	0.1731	146	0.1405	2590	X-RAY DIFFRACTION	100
2.33-2.41	0.2017	151	0.1472	2634	X-RAY DIFFRACTION	100
2.41-2.49	0.1956	135	0.1507	2669	X-RAY DIFFRACTION	100
2.49-2.59	0.2104	106	0.1516	2657	X-RAY DIFFRACTION	100
2.59-2.71	0.1985	130	0.152	2652	X-RAY DIFFRACTION	100
2.71-2.85	0.1952	145	0.1479	2676	X-RAY DIFFRACTION	100
2.85-3.03	0.2023	132	0.1504	2670	X-RAY DIFFRACTION	100
3.03-3.27	0.1564	117	0.1567	2671	X-RAY DIFFRACTION	100
3.27-3.59	0.1969	137	0.1363	2640	X-RAY DIFFRACTION	99
3.59-4.11	0.1641	160	0.1261	2650	X-RAY DIFFRACTION	99
4.11-5.18	0.1361	174	0.116	2667	X-RAY DIFFRACTION	100
5.18-60.26	0.198	149	0.1688	2779	X-RAY DIFFRACTION	99

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	6.2219	-4.2054	-2.0135	3.1702	2.1684	6.787	0.0976	-0.1206	-0.5707	0.0082	-0.0984	0.3505	0.3083	-0.2363	0.1196	0.181	-0.0365	-0.0166	0.1382	0.0371	0.2584	-1.8905	-56.98	41.4282
2	9.7039	-0.8197	-3.5549	1.6849	0.1938	3.0164	0.1485	-0.0015	-0.2815	-0.003	-0.071	0.1241	0.0881	-0.0189	-0.0257	0.2117	0.0027	-0.0306	0.1423	0.007	0.1851	-4.5169	-52.3887	33.4223
3	4.6725	0.0573	1.8104	0.4372	-0.2197	1.278	0.0027	0.0321	-0.058	0.0046	-0	0.0257	0.0381	0.0672	0.0002	0.177	0.0147	0.0052	0.1162	-0.0033	0.1128	-5.841	-40.6982	24.0726
4	1.3902	0.1216	0.3058	0.7542	-0.1804	1.0302	-0.0293	-0.0278	0.0882	0.0109	-0.0088	0.0056	-0.0945	-0.04	0.0459	0.1583	0.0196	0.0037	0.0917	-0.0186	0.1341	-22.3845	-22.9206	14.5577
5	0.7335	-0.3069	0.5607	0.7827	-0.2982	0.7443	0.0292	0.0963	-0.0152	-0.0546	0.0002	0.0309	0.0235	0.0723	-0.033	0.1819	0.0075	0.0061	0.1528	-0.0073	0.1608	-17.3111	-29.4146	9.0944
6	1.3261	0.2634	0.5753	3.0825	-1.3189	1.8093	0.0419	-0.2033	-0.0685	0.078	0.0859	0.2088	0.1478	-0.2165	-0.0771	0.1279	0.034	0.0498	0.1347	-0.029	0.1679	-28.0157	-32.4756	18.426
7	4.4253	4.8893	-1.7031	7.5309	-1.4904	4.3348	-0.019	0.2719	-0.7341	-0.2701	-0.0174	-0.3658	0.2694	0.0703	0.0769	0.2673	0.0758	-0.0331	0.1751	-0.0535	0.2099	-6.816	-49.1076	13.3976
8	3.1579	-0.5273	-0.2661	1.7509	0.1518	1.6529	0.0452	0.0737	-0.2112	-0.0482	-0.0271	0.0317	0.1206	0.0169	-0.0133	0.1466	0.0277	-0.0318	0.0789	0.0254	0.1073	-7.271	-44.7351	26.3112
9	6.9342	-5.4358	-1.5559	7.5632	2.7457	2.4917	0.0066	-0.0721	-0.221	-0.0859	0.0507	0.0169	0.1643	0.1327	-0.0282	0.1436	-0.0048	-0.0105	0.155	0.0051	0.1013	8.6306	-49.4608	38.3528
10	1.4067	-0.689	0.3554	1.7065	0.3943	0.9584	-0.0161	-0.0609	0.1726	-0.0085	-0.0848	-0.0747	-0.0575	0.0179	0.1011	0.1469	-0.0255	0.0021	0.173	0.0254	0.1308	20.244	-37.1999	50.9587
11	1.3306	0.0828	0.7835	0.6296	0.0402	0.9358	0.0777	-0.0519	-0.0065	0.0351	-0.0843	-0.0314	0.0243	-0.0416	0.0082	0.1423	-0.003	0.0073	0.1519	0.0111	0.1093	14.5989	-42.3306	53.3572
12	0.8971	-0.3222	0.5662	1.0522	0.4179	3.8904	-0.0039	0.1797	0.0239	-0.0766	-0.1256	-0.0522	0.1331	0.2149	0.1034	0.1229	-0.028	0.0124	0.1868	0.0242	0.1861	22.8517	-44.1114	42.9523

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 48 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 94 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 95 through 206 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 207 through 280 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 281 through 310 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 27 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 28 through 67 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 68 through 95 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 96 through 177 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 178 through 280 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 281 through 311 )

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