PDB-9yh9: Crystal structure of a phage catechol 1,2-deoxygenase identified ...

ID or keywords:

Entry

Database: PDB / ID: 9yh9

Title

Crystal structure of a phage catechol 1,2-deoxygenase identified from a soil metagenomic survey.

Components

Catechol 1,2-deoxygenase

Keywords

OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Catechol 1 / 2-deoxygenase / metagenome / phage

Function / homology

:

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 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 a phage catechol 1,2-deoxygenase identified from a soil metagenomic survey.
Authors: Lovell, S. / Liu, L. / Buchko, G.W. / Battaile, K.P. / Wu, R. / Cort, J.R. / McClure, R. / Hofmockel, K.S.

History

Deposition	Sep 30, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 8, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9yh9.cif.gz	158.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9yh9.ent.gz	124.1 KB	Display	PDB format
PDBx/mmJSON format	9yh9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9yh9_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9yh9_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9yh9_validation.xml.gz	19.5 KB	Display
Data in CIF	9yh9_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yh/9yh9 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/9yh9	HTTPS FTP

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Related structure data

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: Catechol 1,2-deoxygenase

B: Catechol 1,2-deoxygenase

hetero molecules

41.8 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)	47.745, 56.463, 138.456
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Catechol 1,2-deoxygenase Mass: 20840.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Plasmid: MesoA.00117.a.WU1 / Production host: Escherichia coli BL21(DE3) (bacteria)
#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.24 Å³/Da / Density % sol: 45.06 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Top 96 condition 44: 20% (w/v) PEG MME 5000, 100mM Bis-Tris pH 6.5, Puck: PSL1109, Cryo: 80% crystallant + 20% glycerol.

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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: Dec 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: 1.65→47.74 Å / Num. obs: 45993 / % possible obs: 100 % / Redundancy: 13.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.116 / R_pim(I) all: 0.033 / R_rim(I) all: 0.121 / Χ²: 1.03 / Net I/σ(I): 15.5 / Num. measured all: 603115
Reflection shell	Resolution: 1.65→1.68 Å / % possible obs: 100 % / Redundancy: 13.9 % / R_merge(I) obs: 1.94 / Num. measured all: 30733 / Num. unique obs: 2217 / CC_1/2: 0.413 / R_pim(I) all: 0.537 / R_rim(I) all: 2.014 / Χ²: 1.01 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5533: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→45.14 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2061	2325	5.06 %
R_work	0.1731	-	-
obs	0.1749	45918	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→45.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2708	0	2	254	2964

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2827
X-RAY DIFFRACTION	f_angle_d	1.004	3865
X-RAY DIFFRACTION	f_dihedral_angle_d	16.915	1029
X-RAY DIFFRACTION	f_chiral_restr	0.063	397
X-RAY DIFFRACTION	f_plane_restr	0.01	519

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 (%)
1.65-1.68	0.3473	129	0.2981	2532	X-RAY DIFFRACTION	100
1.68-1.72	0.3158	147	0.2734	2506	X-RAY DIFFRACTION	100
1.72-1.76	0.2998	125	0.2501	2560	X-RAY DIFFRACTION	100
1.76-1.8	0.2634	124	0.2313	2515	X-RAY DIFFRACTION	100
1.8-1.85	0.2576	137	0.2098	2529	X-RAY DIFFRACTION	100
1.85-1.91	0.2036	147	0.1992	2534	X-RAY DIFFRACTION	100
1.91-1.97	0.2508	126	0.1982	2518	X-RAY DIFFRACTION	100
1.97-2.04	0.2397	117	0.1935	2553	X-RAY DIFFRACTION	100
2.04-2.12	0.1982	113	0.1758	2581	X-RAY DIFFRACTION	100
2.12-2.22	0.1836	146	0.166	2534	X-RAY DIFFRACTION	100
2.22-2.33	0.2073	140	0.1638	2547	X-RAY DIFFRACTION	100
2.33-2.48	0.2233	143	0.1713	2550	X-RAY DIFFRACTION	100
2.48-2.67	0.2173	152	0.1743	2570	X-RAY DIFFRACTION	100
2.67-2.94	0.22	128	0.1768	2591	X-RAY DIFFRACTION	100
2.94-3.37	0.1949	141	0.171	2606	X-RAY DIFFRACTION	100
3.37-4.24	0.1841	149	0.1405	2614	X-RAY DIFFRACTION	100
4.24-45.14	0.1779	161	0.1581	2753	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	3.6748	-1.6911	-0.9507	6.3065	1.7101	2.6586	-0.0758	0.2526	0.1455	-0.0091	0.1012	0.1538	-0.1577	0.0835	-0.0171	0.1173	-0.0029	-0.0002	0.2485	0.0307	0.0906	-19.7445	-1.3866	8.6959
2	3.8742	-0.6733	0.0007	6.3793	-0.6302	5.5935	0.0072	0.3583	0.5447	-0.2098	-0.2083	-0.7817	-0.2799	0.5519	0.2196	0.1476	-0.0479	-0.0044	0.3565	0.0122	0.2713	-9.4193	0.9795	9.9326
3	2.5496	-0.9944	0.8757	2.5751	-1.0589	1.9656	0.0572	0.1568	-0.1217	-0.0563	0.0137	0.0472	0.048	-0.1	-0.11	0.15	0.006	0.0026	0.1176	-0.0458	0.125	-16.165	-13.7387	26.1568
4	3.1304	-1.0859	2.419	2.052	-1.3163	8.4086	-0.0157	-0.4073	-0.1297	0.3765	0.263	0.1898	-0.3542	-0.5277	-0.229	0.2233	-0.0419	0.0256	0.1764	0.028	0.2468	-20.554	-16.0422	40.2477
5	1.8815	0.0967	-0.4094	4.0086	-1.7466	2.5362	0.316	0.2522	-0.6214	-0.2777	0.2906	0.5109	0.4109	-0.4593	-0.6023	0.189	-0.0282	-0.0292	0.2106	0.0018	0.2322	-21.2618	-17.1453	27.5325
6	4.4919	0.7155	-1.2694	5.4245	-0.1097	5.1085	0.1453	-0.3958	-0.3151	0.5956	-0.1371	-0.3816	0.1068	0.4703	0.0012	0.2426	0.0027	-0.0774	0.1543	0.0425	0.1922	-4.9687	-20.0814	43.8272
7	2.6074	-2.8385	2.7468	5.4677	-1.5771	4.3644	0.0243	-0.1014	-0.9227	0.0254	0.195	0.9234	-0.0169	-0.5663	-0.1239	0.2246	-0.025	-0.0157	0.1664	-0.0055	0.2952	-21.787	-21.4016	33.8133
8	8.2124	5.7809	0.6495	4.2871	-0.2686	2.0054	0.0321	-0.3407	-0.1378	0.251	-0.1224	-0.1227	-0.1076	-0.0483	0.1391	0.2286	0.0236	-0.0304	0.0748	-0.0169	0.1949	-10.2786	-12.503	41.0475
9	0.3433	0.0883	-0.3243	2.3821	-0.1023	2.196	0.2452	0.0556	-1.0318	0.3482	-0.1981	-0.814	-0.0307	0.3822	-0.0098	0.2865	-0.0239	-0.0992	0.1778	0.0452	0.4301	6.6534	-5.2777	40.3785
10	4.1256	3.1115	2.2885	7.6458	2.6955	4.9366	-0.0191	0.3338	-0.1957	-0.1363	0.2075	0.0521	0.1555	0.1215	-0.1393	0.1434	0.0121	-0.0327	0.1133	-0.0103	0.1908	-13.7549	-17.0167	28.3661
11	7.0779	-0.1664	-0.6756	2.2257	-1.3177	1.7714	0.2908	-0.1346	0.7315	0.2657	-0.1006	0.0093	-0.3471	0.1615	-0.1814	0.2609	-0.0064	-0.0224	0.1191	-0.0493	0.2798	-5.58	-1.6418	37.3384
12	3.7317	0.3253	-0.5705	3.8354	1.5077	5.9379	0.0646	-0.2001	0.1258	0.377	-0.0531	0.0855	-0.0337	-0.3647	-0.0207	0.1894	0.0328	0.002	0.1074	0.0185	0.2191	-19.8463	-6.9093	36.1509
13	6.94	3.8094	2.2803	2.1665	1.031	2.2171	-0.2432	0.0618	-0.3521	0.4253	0.2101	-0.343	0.1515	0.6863	0.0417	0.3516	0.0683	-0.0398	0.3426	-0.0716	0.3017	-1.073	-7.6207	26.6944
14	1.7962	-0.0168	-0.1712	1.9162	-0.2772	2.9599	-0.0459	0.6909	0.0515	-0.2479	0.0008	-0.0988	-0.1112	0.1812	0.053	0.1983	-0.0044	0.0179	0.4625	-0.0046	0.1276	-13.0444	-5.6697	2.9605
15	4.2881	-0.2103	-2.2675	4.516	5.0776	7.9759	-0.0695	1.0392	0.2198	-0.9977	0.1772	0.6047	-0.4924	0.0326	-0.0843	0.3515	0.0016	-0.06	0.5823	0.0795	0.2188	-24.6896	-0.7489	-6.3668
16	2.9501	-1.654	-0.1085	4.1977	-0.1155	2.8623	0.1775	1.1776	0.2496	-0.2955	-0.1128	-0.1335	-0.1396	0.094	-0.0899	0.2575	-0.052	0.0382	0.5001	0.0672	0.1067	-14.9043	-0.9395	0.3982
17	5.5117	-1.8008	0.8587	0.8901	0.543	2.8819	0.085	-0.2515	0.3887	-0.1772	0.1938	1.8551	-0.2527	-1.4281	0.2422	0.3521	0.1381	-0.0674	0.7701	0.2211	1.0554	-35.8529	7.7082	5.7594

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 118 through 150 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 151 through 176 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 4 through 32 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 33 through 50 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 51 through 64 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 65 through 79 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 80 through 89 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 90 through 105 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 106 through 117 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 118 through 136 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 137 through 150 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 151 through 173 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 4 through 13 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 14 through 64 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 65 through 79 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 80 through 105 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 106 through 117 )

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