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

ID or keywords:

Entry

Database: PDB / ID: 9dra

Title

Crystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Iron and 4,5-dichloro-1,2-catechol 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: 1.62 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 (Iron and 4,5-dichloro-1,2-catechol 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 9, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9dra.cif.gz	281.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9dra.ent.gz		Display	PDB format
PDBx/mmJSON format	9dra.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9dra_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	9dra_full_validation.pdf.gz	2.6 MB	Display
Data in XML	9dra_validation.xml.gz	39.6 KB	Display
Data in CIF	9dra_validation.cif.gz	57.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dr/9dra ftp://data.pdbj.org/pub/pdb/validation_reports/dr/9dra	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Catechol 1,2-dioxygenase

B: Catechol 1,2-dioxygenase

hetero molecules

70.7 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)	115.393, 52.306, 120.402
Angle α, β, γ (deg.)	90.00, 92.50, 90.00
Int Tables number	5
Space group name H-M	C121

-
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

-
Non-polymers , 6 types, 849 molecules

#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-A1BA2 / (6R)-3,4-dichloro-6-hydroxycyclohex-3-en-1-one Mass: 181.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₆Cl₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#6: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 837 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
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: 20% 4000, 0.2M CaCl2, 0.1M Tris 8.5 , BumuA.00107.d.A2.PW32075 at 21.7 mg/mL. plate Liu-S-128 A5. Overnight soak in 20mM 4,5-dichloro-1,2-catechol (45C) supplemented with 5mM FeCl2. Partial ...Details: 20% 4000, 0.2M CaCl2, 0.1M Tris 8.5 , BumuA.00107.d.A2.PW32075 at 21.7 mg/mL. plate Liu-S-128 A5. Overnight soak in 20mM 4,5-dichloro-1,2-catechol (45C) supplemented with 5mM FeCl2. Partial 45C occupancy which was modeled as the enol form. Puck: PSL-1902, Cryo: 32% (w/v) 4000, 0.2M CaCl2, 0.1M Tris 8.5

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: 20% 4000, 0.2M CaCl2, 0.1M Tris 8.5 , BumuA.00107.d.A2.PW32075 at 21.7 mg/mL. plate Liu-S-128 A5. Overnight soak in 20mM 4,5-dichloro-1,2-catechol (45C) supplemented with 5mM FeCl2. Partial ...

-
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: 1.62→120.29 Å / Num. obs: 91411 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC_1/2: 0.998 / R_merge(I) obs: 0.102 / R_pim(I) all: 0.045 / R_rim(I) all: 0.111 / Χ²: 0.98 / Net I/σ(I): 10.4 / Num. measured all: 562301
Reflection shell	Resolution: 1.62→1.66 Å / % possible obs: 99.9 % / Redundancy: 6.3 % / R_merge(I) obs: 1.308 / Num. measured all: 42349 / Num. unique obs: 6729 / CC_1/2: 0.787 / R_pim(I) all: 0.56 / R_rim(I) all: 1.426 / Χ²: 1.04 / Net I/σ(I) obs: 1.7

-
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: 1.62→52.89 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1831	4660	5.1 %
R_work	0.1567	-	-
obs	0.158	91343	99.82 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.62→52.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4691	0	93	837	5621

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5124
X-RAY DIFFRACTION	f_angle_d	0.988	6982
X-RAY DIFFRACTION	f_dihedral_angle_d	13.547	1944
X-RAY DIFFRACTION	f_chiral_restr	0.059	759
X-RAY DIFFRACTION	f_plane_restr	0.012	937

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 (%)
1.62-1.64	0.3266	158	0.2899	2874	X-RAY DIFFRACTION	100
1.64-1.66	0.3223	140	0.2732	2849	X-RAY DIFFRACTION	100
1.66-1.68	0.2617	156	0.2591	2906	X-RAY DIFFRACTION	100
1.68-1.7	0.265	142	0.2405	2889	X-RAY DIFFRACTION	100
1.7-1.72	0.2434	164	0.2278	2826	X-RAY DIFFRACTION	100
1.72-1.75	0.2429	161	0.2168	2890	X-RAY DIFFRACTION	100
1.75-1.77	0.2602	185	0.2067	2840	X-RAY DIFFRACTION	100
1.77-1.8	0.2478	169	0.207	2871	X-RAY DIFFRACTION	100
1.8-1.82	0.2521	160	0.1941	2844	X-RAY DIFFRACTION	100
1.82-1.85	0.2383	165	0.2081	2875	X-RAY DIFFRACTION	100
1.85-1.89	0.2335	133	0.1959	2866	X-RAY DIFFRACTION	100
1.89-1.92	0.2078	170	0.1813	2916	X-RAY DIFFRACTION	100
1.92-1.96	0.2156	121	0.171	2864	X-RAY DIFFRACTION	100
1.96-2	0.2127	125	0.1606	2914	X-RAY DIFFRACTION	100
2-2.04	0.183	156	0.1522	2904	X-RAY DIFFRACTION	100
2.04-2.09	0.1712	135	0.1512	2894	X-RAY DIFFRACTION	100
2.09-2.14	0.1881	168	0.1528	2843	X-RAY DIFFRACTION	100
2.14-2.2	0.2263	161	0.1452	2894	X-RAY DIFFRACTION	100
2.2-2.26	0.1912	162	0.1494	2934	X-RAY DIFFRACTION	100
2.26-2.34	0.1634	162	0.1412	2839	X-RAY DIFFRACTION	100
2.34-2.42	0.1538	163	0.143	2863	X-RAY DIFFRACTION	100
2.42-2.52	0.174	129	0.1395	2947	X-RAY DIFFRACTION	100
2.52-2.63	0.1853	143	0.1386	2926	X-RAY DIFFRACTION	100
2.63-2.77	0.1653	170	0.144	2864	X-RAY DIFFRACTION	100
2.77-2.94	0.1689	181	0.1448	2871	X-RAY DIFFRACTION	100
2.94-3.17	0.1762	159	0.15	2885	X-RAY DIFFRACTION	99
3.17-3.49	0.1617	136	0.1447	2946	X-RAY DIFFRACTION	99
3.49-3.99	0.1417	159	0.1355	2891	X-RAY DIFFRACTION	99
4-5.03	0.1507	156	0.1193	2944	X-RAY DIFFRACTION	100
5.03-52.89	0.1818	171	0.1783	3014	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	6.7396	-3.3363	-0.9158	5.8552	1.3141	4.0971	-0.0195	-0.3028	-0.683	0.2049	0.0418	0.3938	0.5227	-0.1151	0.002	0.2968	-0.0351	-0.0762	0.2198	0.0593	0.3339	-1.8436	-57.0626	41.3111
2	1.3292	-0.5741	0.7364	0.3686	-0.5356	0.7912	0.0846	0.0066	-0.1328	-0.0197	-0.0003	0.0374	0.0998	0.0295	-0.087	0.2434	0.0059	-0.0437	0.1513	-0.0134	0.2078	-8.9825	-42.7623	25.3094
3	1.9235	0.4134	-0.2313	1.5987	-0.2155	1.6176	-0.083	-0.0277	0.1256	-0.0033	-0.0008	0.0999	-0.1966	-0.1301	0.0744	0.2214	0.0471	-0.032	0.1422	-0.0202	0.2071	-28.5548	-21.5141	12.5242
4	1.4383	-0.1929	0.3423	0.9203	-0.1281	1.0231	-0.0225	-0.024	0.1055	0.0032	-0.0515	-0.1062	-0.1196	0.0532	0.0747	0.2381	0.006	-0.0388	0.1327	-0.008	0.2187	-17.3457	-20.411	15.0858
5	0.774	-0.047	0.6161	0.7203	-0.2513	1.0105	0.0476	0.0945	-0.0563	-0.0207	-0.0248	0.0529	0.0287	0.0584	-0.0221	0.2014	0.0117	-0.0201	0.1477	-0.0111	0.1801	-17.3462	-29.4696	9.0809
6	1.6686	0.1395	0.5616	2.4122	-0.6732	2.4605	0.031	-0.2825	-0.0654	0.2042	0.0452	0.1504	0.1162	-0.2859	-0.0328	0.1583	0.0214	0.0212	0.1517	-0.0187	0.1889	-28.0149	-32.5132	18.4063
7	8.4211	3.1889	0.0139	4.396	-0.4881	2.8298	-0.0391	0.4312	-0.5741	-0.3446	0.1124	-0.0815	0.4512	0.1221	-0.0639	0.3633	0.0769	-0.0899	0.1827	-0.0691	0.2613	-6.8585	-49.1889	13.287
8	2.0543	-1.0629	0.993	0.6675	-0.2509	1.0768	0.1061	-0.045	-0.1687	-0.0535	-0.0031	0.0209	0.0725	0.0507	-0.1064	0.2171	-0.0091	-0.0363	0.1444	0.0156	0.2082	-1.1906	-46.5409	30.8487
9	1.0777	-0.1896	0.5455	1.3166	0.337	1.2055	-0.0391	-0.0551	0.1455	-0.0124	-0.0798	-0.0285	-0.0871	-0.0284	0.1093	0.2066	-0.0282	-0.0219	0.2181	0.026	0.1987	19.788	-37.3117	51.4612
10	0.9351	-0.0486	0.489	0.6682	0.1428	0.8192	0.1055	-0.0578	-0.0616	0.0552	-0.0565	-0.0008	0.0271	-0.073	-0.062	0.2047	-0.0162	-0.0227	0.2208	0.0252	0.1796	12.9769	-44.5623	53.3397
11	1.0221	-0.0673	0.3052	0.6887	0.028	2.6427	-0.0336	0.1927	0.0106	-0.0878	-0.1159	-0.0532	0.0023	0.2396	0.1531	0.2319	-0.0241	-0.0347	0.2295	0.0344	0.2417	22.9184	-44.1806	42.8417

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 114 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 115 through 157 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 158 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 95 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 96 through 206 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 207 through 280 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 281 through 311 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 849 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 6 types, 849 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 849 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi