PDB-6b9r: Streptomyces albus HEPD with substrate 2-hydroxyethylphosphonate ...

ID or keywords:

Entry

Database: PDB / ID: 6b9r

Title

Streptomyces albus HEPD with substrate 2-hydroxyethylphosphonate (2-HEP) and Fe(II) bound

Components

Hydroxyethylphosphonate dioxygenase

Keywords

OXIDOREDUCTASE / Phosphonate / Hydroxymethylphosphonate / Iron

Function / homology

(2-hydroxyethyl)phosphonic acid / :

Function and homology information

Biological species

Streptomyces albus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.802 Å

Authors

Born, D.A. / Drennan, C.L.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	1S10RR029205-01	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	3P41GM103403-15S1	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	5T32GM008313-29	United States

Citation

Journal: Science / Year: 2017
Title: Structural basis for methylphosphonate biosynthesis.
Authors: Born, D.A. / Ulrich, E.C. / Ju, K.S. / Peck, S.C. / van der Donk, W.A. / Drennan, C.L.

History

Deposition	Oct 11, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6b9r.cif.gz	713.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6b9r.ent.gz	589 KB	Display	PDB format
PDBx/mmJSON format	6b9r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6b9r_validation.pdf.gz	3.8 MB	Display	wwPDB validaton report
Full document	6b9r_full_validation.pdf.gz	3.8 MB	Display
Data in XML	6b9r_validation.xml.gz	80.2 KB	Display
Data in CIF	6b9r_validation.cif.gz	123.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b9/6b9r ftp://data.pdbj.org/pub/pdb/validation_reports/b9/6b9r	HTTPS FTP

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Related structure data

Related structure data	6b9sC 6b9tC C: citing same article (ref.)
Similar structure data	4tri-d 3g5h-2 3cxz-1 4g48-2 4iq9-2 6mo3-d 3cxv-1 2bvj-d 4ipw-2 4jad-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hydroxyethylphosphonate dioxygenase

B: Hydroxyethylphosphonate dioxygenase

C: Hydroxyethylphosphonate dioxygenase

D: Hydroxyethylphosphonate dioxygenase

hetero molecules

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

1

A: Hydroxyethylphosphonate dioxygenase

D: Hydroxyethylphosphonate dioxygenase

hetero molecules

defined by author&software
Evidence: gel filtration
99.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hydroxyethylphosphonate dioxygenase

C: Hydroxyethylphosphonate dioxygenase

hetero molecules

defined by author&software
99.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.238, 100.707, 99.088
Angle α, β, γ (deg.)	90.00, 92.27, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hydroxyethylphosphonate dioxygenase Mass: 49475.406 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces albus (bacteria) / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta (DE3)
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-2HE / (2-hydroxyethyl)phosphonic acid Mass: 126.048 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₇O₄P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1951 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	The database reference sequence for the studied protein can be found by UniParc ID UPI0005175950 or ...The database reference sequence for the studied protein can be found by UniParc ID UPI0005175950 or NCBI RefSeq WP_032782080.1.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.29 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 255 mM sodium malate, 24% (w/v) PEG 3350, 4 mM 2-hydroxyethylphosphonate. Soaking was performed with 2 mM iron(II)ammonium sulfate.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 6, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.8→100 Å / Num. obs: 156962 / % possible obs: 97.7 % / Redundancy: 4.1 % / R_pim(I) all: 0.006 / R_rim(I) all: 0.012 / Net I/σ(I): 11.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing
SHARP		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 1.802→89.168 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.3

	R_factor	Num. reflection	% reflection
R_free	0.1887	7702	4.91 %
R_work	0.1524	-	-
obs	0.1542	156919	97.25 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.802→89.168 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13601	0	92	1951	15644

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	14061
X-RAY DIFFRACTION	f_angle_d	0.827	19181
X-RAY DIFFRACTION	f_dihedral_angle_d	16.893	8357
X-RAY DIFFRACTION	f_chiral_restr	0.05	2082
X-RAY DIFFRACTION	f_plane_restr	0.006	2534

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 (%)
1.8021-1.8226	0.2999	199	0.249	4087	X-RAY DIFFRACTION	80
1.8226-1.8441	0.2803	253	0.2316	4788	X-RAY DIFFRACTION	94
1.8441-1.8666	0.2954	233	0.2195	4902	X-RAY DIFFRACTION	95
1.8666-1.8902	0.2573	256	0.2098	4896	X-RAY DIFFRACTION	97
1.8902-1.9151	0.25	241	0.2051	4957	X-RAY DIFFRACTION	97
1.9151-1.9413	0.2474	259	0.1965	5009	X-RAY DIFFRACTION	98
1.9413-1.969	0.2398	255	0.1891	4979	X-RAY DIFFRACTION	98
1.969-1.9984	0.2492	293	0.1802	4878	X-RAY DIFFRACTION	98
1.9984-2.0296	0.2062	282	0.18	4980	X-RAY DIFFRACTION	97
2.0296-2.0629	0.2548	245	0.1689	4934	X-RAY DIFFRACTION	96
2.0629-2.0985	0.2133	281	0.1649	5012	X-RAY DIFFRACTION	99
2.0985-2.1367	0.2138	275	0.1609	5064	X-RAY DIFFRACTION	99
2.1367-2.1778	0.2071	264	0.1566	5003	X-RAY DIFFRACTION	99
2.1778-2.2222	0.1939	281	0.1506	4997	X-RAY DIFFRACTION	99
2.2222-2.2705	0.1958	240	0.1475	5017	X-RAY DIFFRACTION	98
2.2705-2.3234	0.1973	252	0.1478	5053	X-RAY DIFFRACTION	99
2.3234-2.3815	0.1944	254	0.1566	5044	X-RAY DIFFRACTION	99
2.3815-2.4459	0.211	244	0.1561	5034	X-RAY DIFFRACTION	98
2.4459-2.5178	0.1923	216	0.1522	4940	X-RAY DIFFRACTION	96
2.5178-2.5991	0.1969	318	0.152	4982	X-RAY DIFFRACTION	99
2.5991-2.692	0.2	268	0.1492	5078	X-RAY DIFFRACTION	99
2.692-2.7998	0.174	244	0.1477	5073	X-RAY DIFFRACTION	99
2.7998-2.9272	0.1976	225	0.1513	5084	X-RAY DIFFRACTION	99
2.9272-3.0816	0.1741	234	0.1456	5090	X-RAY DIFFRACTION	99
3.0816-3.2747	0.1799	227	0.1434	4970	X-RAY DIFFRACTION	97
3.2747-3.5275	0.1629	249	0.1345	5140	X-RAY DIFFRACTION	99
3.5275-3.8825	0.152	279	0.1288	5039	X-RAY DIFFRACTION	99
3.8825-4.4443	0.1524	319	0.1249	5018	X-RAY DIFFRACTION	98
4.4443-5.5992	0.1493	265	0.1315	5026	X-RAY DIFFRACTION	97
5.5992-89.2772	0.1948	251	0.172	5143	X-RAY DIFFRACTION	98

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	0.0317	0.0669	-0.0933	0.2067	-0.1968	0.177	-0.0269	0.0193	-0.1852	0.027	-0.0817	0.0022	0.2694	-0.3225	0.0001	0.2228	-0.0472	0.0405	0.2981	0.005	0.227	-16.1825	109.8643	27.6742
2	0.2064	0.0317	0.1584	0.0142	0.018	0.1883	-0.0031	0.0361	-0.0112	-0.0348	0.0086	-0.0185	0.0307	-0.1305	0	0.1999	-0.0205	0.0177	0.2039	0.0121	0.2101	-14.4853	112.8791	18.0381
3	0.9757	-0.107	0.1015	0.713	0.0463	0.2676	0.0035	0.3072	0.1822	-0.1523	0.0185	0.1189	-0.0146	-0.0944	-0.0001	0.2397	0.0212	-0.0042	0.274	0.0425	0.1971	3.186	118.8026	-12.6404
4	0.3817	0.1539	-0.0443	0.2376	0.1163	0.0186	0.0484	0.1323	0.1215	-0.0941	0.0877	-0.1114	-0.077	-0.1207	0.0002	0.237	0.0163	0.0067	0.2457	0.0358	0.2025	4.8225	121.2145	-3.9083
5	0.6357	0.091	-0.334	0.4887	0.1681	0.2304	-0.012	-0.1057	0.0436	0.0425	0.0488	-0.2392	-0.0718	0.0868	0	0.1689	-0.02	-0.0243	0.1811	0.025	0.2611	22.0385	131.8834	22.158
6	0.1323	-0.1349	0.2036	0.073	0.0519	0.1408	0.0022	0.0134	0.0945	-0.1266	0.0087	-0.1011	-0.0345	-0.0662	0	0.2094	-0.023	0.0311	0.2248	0.0054	0.2835	20.1066	121.5791	4.473
7	0.5202	-0.4826	-0.222	0.6999	0.0503	0.5286	0.0064	0.0657	-0.1256	-0.0312	-0.0339	0.0543	0.1024	-0.0085	-0	0.205	-0.0042	-0.003	0.1693	-0.0139	0.1493	11.3955	100.0006	-1.4287
8	0.4012	-0.172	-0.162	0.4391	0.2491	0.1017	-0.0861	-0.1262	-0.0991	0.0662	0.0448	0.0414	0.2672	0.098	0.0001	0.2635	0.0009	0.0184	0.2747	-0.0043	0.2012	4.7708	105.4402	16.2246
9	0.2759	0.1298	-0.0489	0.3555	0.1013	0.5697	0.0824	-0.0478	0.101	0.0331	0.0396	-0.0474	-0.1174	0.0951	0.0168	0.1611	-0.0115	0.0266	0.114	-0.0051	0.1653	54.4874	127.943	-23.8698
10	0.6707	-0.0229	0.0249	0.3181	-0.3036	0.2156	0.0638	-0.1003	0.0836	0.0644	0.1054	0.0522	-0.0868	-0.122	0.022	0.2146	0.0005	0.054	0.138	0.0061	0.1818	34.4066	130.0149	-14.7657
11	0.1707	0.0529	0.0349	0.138	-0.0214	0.6491	0.0128	-0.0601	-0.0295	0.0304	-0.0004	0.0241	0.0055	-0.0822	0	0.1615	0.0035	0.0026	0.1283	0.0062	0.1398	39.9683	111.2365	-20.0887
12	0.6434	-0.3516	0.4849	0.3606	-0.0894	0.3861	-0.0273	0.101	0.052	-0.0852	-0.0007	-0.0135	-0.1114	0.1945	0	0.2376	-0.0346	0.0492	0.1091	-0.0083	0.1869	51.4217	140.0994	-28.43
13	0.1077	0.1846	-0.0077	0.1858	-0.0144	0.1188	0.0006	0.0516	0.0042	-0.0585	0.0212	-0.1164	-0.0116	0.0469	-0.0096	0.1382	0.005	0.0264	0.09	-0.0067	0.1242	58.9556	115.6073	-46.0952
14	0.3714	0.3886	0.314	0.6223	0.0015	0.1829	-0.015	0.0444	-0.027	-0.0806	0.0025	-0.0315	0.0524	-0.0072	0	0.1551	0.0164	0.0153	0.1303	-0.009	0.137	54.7444	100.9992	-46.5016
15	0.328	-0.1614	0.0973	0.1172	0.2153	0.3791	-0.0795	-0.0674	-0.0216	0.02	-0.0163	0.0382	0.0393	-0.0264	-0	0.1698	-0.008	0.0155	0.1118	-0.0196	0.1563	37.9274	98.9397	-23.0219
16	1.1021	0.4991	-0.4009	0.8171	-0.086	0.3717	-0.0192	0.2155	0.0564	-0.1604	0.0551	0.1894	0.003	-0.1553	-0.0007	0.1701	0.0157	-0.0283	0.1882	0.0159	0.1412	38.1868	113.9773	-56.1838
17	0.3076	-0.1326	0.091	0.4752	0.4803	0.5802	0.0755	0.0453	0.1216	-0.1213	-0.1126	0.1819	-0.3101	-0.2865	0.1428	0.2609	-0.0018	0.0656	0.1676	-0.0154	0.1909	38.4604	124.4972	-35.7735
18	0.0687	0.0671	-0.0476	0.4164	-0.1291	0.1483	0.0306	0.0225	-0.01	-0.2281	-0.0583	0.1884	-0.1554	-0.06	0	0.2235	0.0219	-0.0463	0.2355	0.0051	0.2444	-14.2247	124.2036	-0.3684
19	0.4619	-0.0889	0.2731	0.2741	-0.0619	0.5832	-0.0392	-0.1084	0.0033	0.0775	0.0417	0.0339	-0.0272	-0.1102	-0	0.1649	0.0111	0.0175	0.1953	0.0146	0.1671	-5.4612	118.3072	34.1973
20	0.756	-0.0082	0.418	0.4631	-0.2896	0.3007	-0.0442	-0.0735	-0	0.0552	0.0182	0.0123	-0.0505	-0.0516	-0	0.1963	0.0091	0.0109	0.2015	0.0108	0.1817	0.9967	115.1408	34.9764
21	0.3852	0.0848	0.0024	0.2291	0.1959	0.3673	-0.0304	-0.0777	-0.0262	-0.0077	0.036	0.0168	0.0183	0.0596	0	0.1932	0.0199	0.0086	0.1772	0.0163	0.1594	23.2354	107.8808	15.1033
22	0.174	0.0277	-0.2002	0.4066	-0.2369	0.2673	-0.0324	-0.1415	0.1987	0.101	-0.1928	-0.4822	-0.1834	0.2068	-0.4593	0.2152	-0.0304	-0.0691	0.2428	0.0067	0.3048	16.0128	132.3653	39.7098
23	0.9103	-0.0542	0.1273	0.3417	0.1004	0.4258	-0.1073	-0.0123	0.2324	0.0182	0.0461	-0.0707	-0.2134	0.0568	-0	0.2417	0.0088	-0.0298	0.1633	-0.0036	0.1982	3.475	137.0425	32.9464
24	0.3964	0.0645	0.258	0.4785	0.2116	0.2392	-0.0554	0.1793	0.1194	-0.1203	-0.0254	0.0065	-0.2771	0.2276	0	0.2498	0.0089	-0.0119	0.2987	0.0139	0.2441	3.4387	129.5257	12.3124

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 51 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 85 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 86 through 180 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 181 through 223 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 224 through 288 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 289 through 316 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 317 through 407 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 408 through 450 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 9 through 151 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 152 through 223 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 224 through 450 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 5 through 51 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 52 through 151 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 152 through 223 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 224 through 316 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 317 through 411 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 412 through 450 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 9 through 51 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 52 through 180 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 181 through 223 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 224 through 306 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 307 through 332 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 333 through 411 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 412 through 450 )

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Open data

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Download

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Validation report

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Assembly

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About Yorodumi

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

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Yorodumi