PDB-6eb0: STRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGE...

ID or keywords:

Entry

Database: PDB / ID: 6eb0

Title

STRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGENASE COMPONENT FROM ESCHERICHIA COLI

Components

4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit

Keywords

OXIDOREDUCTASE / PROTEIN ENGINEERING: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE / OXYGENASE COMPONENT

Function / homology

Function and homology information

4-hydroxyphenylacetate 3-monooxygenase / oxidoreductase activity, acting on the CH-CH group of donors / phenylacetate catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.37 Å

Authors

Zhou, D. / Kandavelu, P. / Zhang, H. / Wang, B.C. / Yan, Y. / Rose, J.

Citation

Journal: Sci Rep / Year: 2019
Title: Structural Insights into Catalytic Versatility of the Flavin-dependent Hydroxylase (HpaB) from Escherichia coli.
Authors: Shen, X. / Zhou, D. / Lin, Y. / Wang, J. / Gao, S. / Kandavelu, P. / Zhang, H. / Zhang, R. / Wang, B.C. / Rose, J. / Yuan, Q. / Yan, Y.

History

Deposition	Aug 3, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 22, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6eb0.cif.gz	801.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6eb0.ent.gz	666.3 KB	Display	PDB format
PDBx/mmJSON format	6eb0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6eb0_validation.pdf.gz	478 KB	Display	wwPDB validaton report
Full document	6eb0_full_validation.pdf.gz	508.7 KB	Display
Data in XML	6eb0_validation.xml.gz	79.7 KB	Display
Data in CIF	6eb0_validation.cif.gz	112.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eb/6eb0 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/6eb0	HTTPS FTP

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Related structure data

Related structure data	6b1bC 2yygS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6b1b-1 6qyi-1 6qyh-1 4oo2-d 4743 4il0-1 4il0-2 2wva-1 Search similar-shape structures by Omokage search (details) 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: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit

B: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit

C: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit

D: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit

hetero molecules

240 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	179.409, 93.734, 142.335
Angle α, β, γ (deg.)	90.00, 108.23, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit Mass: 59926.652 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria) Strain: B / BL21-DE3 / Gene: ECBD_3674 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140NG21
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 833 / 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: 2.54 Å³/Da / Density % sol: 51.66 %
Crystal grow	Temperature: 291 K / Method: microbatch / pH: 6.5 Details: MICRO BATCH UNDER OIL AT 291K USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SODIUM CONCENTRATE AND A PRECIPITANT COCKTAIL CONTAINING 0.08 M CACODYLATE BUFFER CONTAINING 0.16 M ...Details: MICRO BATCH UNDER OIL AT 291K USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SODIUM CONCENTRATE AND A PRECIPITANT COCKTAIL CONTAINING 0.08 M CACODYLATE BUFFER CONTAINING 0.16 M MAGNESIUM ACETATE TETRAHYDRATE, 16% POLYETHYLENE GLYCOL 8000, AND 20% V/V GLYCEROL, PH 6.0, MICROBATCH UNDER OIL PH range: 6.5

Crystal

Density Matthews: 2.54 Å³/Da / Density % sol: 51.66 %

Crystal grow

Temperature: 291 K / Method: microbatch / pH: 6.5
Details: MICRO BATCH UNDER OIL AT 291K USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SODIUM CONCENTRATE AND A PRECIPITANT COCKTAIL CONTAINING 0.08 M CACODYLATE BUFFER CONTAINING 0.16 M ...
PH range: 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2013 / Details: Rosenbaum Optics
Radiation	Monochromator: SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.37→46.363 Å / Num. obs: 90432 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / R_merge(I) obs: 0.113 / Net I/σ(I): 15.81
Reflection shell	Resolution: 2.37→2.46 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.475 / Mean I/σ(I) obs: 3.27 / % possible all: 93.5

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
SCALEPACK		data scaling
BALBES		phasing
PHENIX	1.10.1_2155	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2YYG

2yyg

Resolution: 2.37→46.363 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.59

	R_factor	Num. reflection	% reflection
R_free	0.1954	4400	4.87 %
R_work	0.1598	-	-
obs	0.1615	90403	99.25 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.37→46.363 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16396	0	12	833	17241

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	16797
X-RAY DIFFRACTION	f_angle_d	0.85	22777
X-RAY DIFFRACTION	f_dihedral_angle_d	10.933	9980
X-RAY DIFFRACTION	f_chiral_restr	0.053	2420
X-RAY DIFFRACTION	f_plane_restr	0.006	2979

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 (%)
2.3704-2.3973	0.2928	140	0.1955	2397	X-RAY DIFFRACTION	83
2.3973-2.4255	0.2697	149	0.1999	2808	X-RAY DIFFRACTION	98
2.4255-2.4551	0.2526	167	0.196	2836	X-RAY DIFFRACTION	99
2.4551-2.4862	0.2372	157	0.1907	2793	X-RAY DIFFRACTION	99
2.4862-2.5189	0.2278	139	0.1906	2896	X-RAY DIFFRACTION	100
2.5189-2.5534	0.2325	139	0.1882	2837	X-RAY DIFFRACTION	100
2.5534-2.5899	0.2446	139	0.1855	2920	X-RAY DIFFRACTION	100
2.5899-2.6285	0.249	131	0.1764	2852	X-RAY DIFFRACTION	100
2.6285-2.6696	0.2286	144	0.1766	2918	X-RAY DIFFRACTION	100
2.6696-2.7134	0.2272	170	0.1791	2794	X-RAY DIFFRACTION	100
2.7134-2.7601	0.2532	136	0.177	2915	X-RAY DIFFRACTION	100
2.7601-2.8103	0.2016	161	0.1694	2870	X-RAY DIFFRACTION	100
2.8103-2.8644	0.2066	150	0.1619	2852	X-RAY DIFFRACTION	100
2.8644-2.9228	0.2037	161	0.1605	2875	X-RAY DIFFRACTION	100
2.9228-2.9864	0.2131	146	0.1565	2901	X-RAY DIFFRACTION	100
2.9864-3.0558	0.2024	137	0.1595	2885	X-RAY DIFFRACTION	100
3.0558-3.1322	0.2283	141	0.1595	2877	X-RAY DIFFRACTION	100
3.1322-3.2169	0.1758	149	0.1601	2875	X-RAY DIFFRACTION	100
3.2169-3.3115	0.1696	147	0.1532	2889	X-RAY DIFFRACTION	100
3.3115-3.4184	0.1796	156	0.1503	2858	X-RAY DIFFRACTION	100
3.4184-3.5405	0.2142	130	0.1476	2927	X-RAY DIFFRACTION	100
3.5405-3.6822	0.1662	148	0.1404	2859	X-RAY DIFFRACTION	100
3.6822-3.8497	0.165	153	0.1453	2920	X-RAY DIFFRACTION	100
3.8497-4.0526	0.1639	143	0.1417	2915	X-RAY DIFFRACTION	100
4.0526-4.3063	0.1525	146	0.1352	2865	X-RAY DIFFRACTION	100
4.3063-4.6385	0.1615	145	0.1422	2919	X-RAY DIFFRACTION	100
4.6385-5.1048	0.1848	133	0.1552	2904	X-RAY DIFFRACTION	100
5.1048-5.8422	0.2101	155	0.1726	2918	X-RAY DIFFRACTION	100
5.8422-7.3559	0.2465	148	0.1876	2933	X-RAY DIFFRACTION	100
7.3559-46.3721	0.1698	140	0.1576	2995	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	0.0649	0.014	-0.0599	0.0415	-0.094	0.1183	-0.0813	0.2603	0.0631	-0.3946	0.1129	-0.1628	-0.3091	0.0292	-0	0.3976	-0.0383	0.034	0.3922	0.0011	0.3581	43.7819	3.7582	-7.1227
2	0.4777	0.0067	-0.035	0.4894	-0.1261	0.2835	-0.0635	0.0441	-0.0435	-0.0822	0.0495	0.0293	0.0801	-0.0209	-0	0.3819	-0.013	-0.0089	0.3321	-0.0092	0.3148	32.2285	0.8259	-0.7641
3	-0.0592	-0.1297	0.0503	0.1606	-0.0657	0.2589	-0.014	0.0342	-0.0289	-0.0104	0.0072	0.0772	-0.0473	0.0152	-0	0.3722	-0.0328	-0.0145	0.337	0.0154	0.3554	32.4434	15.1552	4.5364
4	0.3624	0.3441	-0.1318	0.4398	0.1452	0.3077	-0.0471	0.0218	0.0122	0.0676	-0.0038	0.0393	0.0079	-0.0187	0	0.3405	-0.0194	0.0265	0.3119	-0.012	0.345	25.3875	-10.1196	17.381
5	0.1561	-0.0174	-0.066	0.3417	0.0581	-0.0087	-0.0243	0.0189	-0.0353	-0.0156	0.0219	0.0386	0.0875	-0.0206	0	0.3473	0.0218	0.005	0.3472	0.0014	0.3542	47.072	-10.0481	26.1598
6	0.1503	-0.3203	-0.0973	0.347	0.1385	0.3743	-0.0597	0.0974	0.1075	-0.167	0.0045	0.1687	0.0789	-0.1642	0	0.3527	-0.043	-0.0436	0.4395	-0.0195	0.4139	-7.2117	-4.1213	25.5423
7	0.0625	-0.0721	-0.05	0.1251	0.0664	0.0254	-0.0883	-0.1566	0.151	0.174	0	0.0787	-0.1249	-0.3951	-0	0.353	0.0325	0.027	0.4563	-0.0225	0.4267	-9.388	7.4679	68.112
8	0.2767	-0.2016	-0.1627	0.6198	-0.1869	0.2545	-0.0934	-0.1016	-0.0201	0.0278	0.0724	-0.025	0.0261	-0.0345	0	0.338	0.0218	0.0067	0.4012	0.0029	0.3414	2.507	9.2934	62.1679
9	0.0363	0.0435	0.0528	0.1976	0.2089	0.0709	-0.0203	0.0297	-0.0971	-0.2169	0.0366	0.0103	-0.0318	-0.0017	-0.0001	0.4351	0.0317	0.0009	0.4709	-0.0355	0.3627	-7.661	20.9594	47.3437
10	0.0164	-0.1123	0.0736	0.1944	0.0384	0.369	-0.0666	-0.0434	0.0017	-0.0389	-0.0133	0.02	-0.0155	-0.0515	-0	0.3211	0.0149	0.006	0.4107	-0.0119	0.3862	-4.232	11.9953	52.0705
11	0.6774	-0.0872	-0.1061	0.139	0.1203	0.3749	-0.0271	-0.0547	-0.0019	-0.0052	0.01	0.0116	0.0297	-0.007	-0	0.3308	0.0333	0.0089	0.3552	0.0149	0.3154	17.7707	-2.4296	51.1351
12	0.2532	-0.0131	0.164	0.0459	-0.1188	0.4726	-0.0144	-0.1273	0.0376	0.2259	-0.0198	-0.1246	0.1506	0.0167	0.0001	0.4402	0.0036	0.0495	0.3592	0.0425	0.3957	2.7017	-20.0797	47.9201
13	-0.0196	-0.018	0.0365	0.1531	-0.1538	0.3958	0.0224	-0.0467	0.0358	0.037	-0.0188	-0.0198	-0.1268	0.0193	0	0.3812	-0.0191	-0.0172	0.3281	-0.0257	0.364	40.6762	17.0679	34.9884
14	0.3723	0.0144	0.2051	0.5439	-0.1519	0.426	-0.0208	-0.0814	0.0339	0.0397	0.0481	-0.0611	-0.0789	0.0503	-0	0.3182	0.0018	-0.0181	0.3623	0.0049	0.3221	53.5045	2.5578	52.6145
15	0.0672	-0.0196	0.0431	-0.0176	-0.0196	0.1818	0.0162	-0.0823	-0.0186	-0.0622	0.0886	-0.1412	0.0905	-0.0393	0	0.3889	0.0054	-0.0309	0.3608	0.037	0.3769	55.9731	-18.1203	47.4216
16	0.2463	0.0301	0.3536	0.1208	-0.1908	0.2919	0.0266	-0.0342	-0.0554	0.002	0.0405	0.0395	0.009	0.023	-0	0.3491	0.0252	0.01	0.3727	0.0216	0.3612	53.4539	-7.9137	45.8187
17	0.388	0.2005	-0.2303	0.2037	-0.0343	0.27	-0.0533	-0.0493	-0.0041	-0.0159	0.0251	0.0027	0.0401	0.021	-0	0.316	0.025	-0.0093	0.3171	0.0123	0.3277	27.5856	2.6541	41.6055
18	0.4375	-0.0667	0.1695	0.3588	0.1548	0.0934	0.0679	0.0502	-0.0278	0.015	0.0416	0.1273	0.1822	-0.1281	0	0.428	-0.0782	0.0163	0.4322	-0.0034	0.4979	-13.6536	-27.7409	23.3683
19	0.1637	-0.0774	0.1063	0.1902	-0.0411	0.3106	-0.0268	0.0973	-0.0304	-0.0549	-0.011	0.0112	0.1301	-0.1275	0	0.4642	-0.053	0.0314	0.3836	-0.0137	0.441	0.4402	-30.4985	14.3495
20	0.0936	-0.042	-0.0373	0.0848	0.0521	0.0255	-0.0445	0.0327	0.028	0.024	0.2422	-0.0302	0.0038	0.0644	-0	0.5878	0.009	0.0002	0.3762	-0.0121	0.4823	6.4449	-39.8399	38.9993
21	0.0675	0.0118	0.0967	0.2933	-0.0312	0.132	0.0292	0.0204	-0.0354	0.0577	-0.0505	0.037	0.1465	-0.0226	0	0.5026	-0.044	0.0219	0.3684	0.0175	0.4556	0.8845	-34.3527	31.963
22	0.34	0.0911	0.0685	0.2764	-0.2531	0.584	-0.0535	-0.0153	-0.0462	0.0578	0.0524	-0.017	0.0452	-0.0021	0	0.3143	-0.043	-0.0017	0.3334	-0.0059	0.344	9.0249	-10.0648	21.4143
23	0.2479	-0.0188	-0.0651	0.0707	-0.1302	0.1914	-0.0984	-0.0287	-0.0287	-0.0284	0.0558	-0.0003	0.0148	-0.1102	0	0.354	-0.0128	-0.0318	0.4455	0.0064	0.3987	-6.7982	-0.6675	35.8089
24	0.216	-0.2375	-0.0017	0.2035	0.1952	0.354	-0.0287	0.1092	-0.1288	0.0121	0.0382	-0.0643	0.0992	0.0402	0	0.3607	0.0139	-0.0073	0.3411	-0.013	0.3429	42.6433	-14.3679	17.2531

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 30 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 167 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 168 through 300 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 301 through 396 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 397 through 464 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 465 through 519 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 30 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 31 through 167 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 168 through 217 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 218 through 300 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 301 through 396 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 397 through 464 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 465 through 519 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 2 through 167 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 168 through 217 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 218 through 300 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 301 through 519 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 2 through 71 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 72 through 149 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 150 through 182 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 183 through 300 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 301 through 396 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 397 through 464 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 465 through 519 )

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-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

-
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