PDB-6onn: Crystal structure of 8-amino-7-oxononanoate synthase from Burkhol...

ID or keywords:

Entry

Database: PDB / ID: 6onn

Title

Crystal structure of 8-amino-7-oxononanoate synthase from Burkholderia phymatum

Components

8-amino-7-oxononanoate synthase

Keywords

TRANSFERASE / SSGCID / 8-amino-7-oxononanoate synthase / Burkholderia phymatum / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function

Biological species

Paraburkholderia phymatum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be published
Title: Crystal structure of 8-amino-7-oxononanoate synthase from Burkholderia phymatum
Authors: Conrady, D.G. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Apr 22, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 1, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6onn.cif.gz	316.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6onn.ent.gz	253 KB	Display	PDB format
PDBx/mmJSON format	6onn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6onn_validation.pdf.gz	436.7 KB	Display	wwPDB validaton report
Full document	6onn_full_validation.pdf.gz	439.9 KB	Display
Data in XML	6onn_validation.xml.gz	34.9 KB	Display
Data in CIF	6onn_validation.cif.gz	53.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/on/6onn ftp://data.pdbj.org/pub/pdb/validation_reports/on/6onn	HTTPS FTP

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Related structure data

Related structure data	5jayS S: Starting model for refinement
Similar structure data	5vnx-3 5jay-2 1g4x-d 2qbt-d 6t3v-d 2jg2-d 5jay-1 5vnx-2 5vrd-1 5d8g-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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 8-amino-7-oxononanoate synthase

B: 8-amino-7-oxononanoate synthase

85.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 8-amino-7-oxononanoate synthase

defined by author
42.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 8-amino-7-oxononanoate synthase

defined by author
42.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.700, 92.580, 125.560
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid -1 through 8 or resid 10...
2	1	(chain B and (resid -1 through 8 or resid 10...

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	HIS	GLU	GLU	(chain A and (resid -1 through 8 or resid 10...	A	A	-1 - 8	7 - 16
1	2	GLY	GLY	ALA	ALA	(chain A and (resid -1 through 8 or resid 10...	A	A	10 - 61	18 - 69
1	3	THR	THR	THR	THR	(chain A and (resid -1 through 8 or resid 10...	A	A	63	71
1	4	GLY	GLY	GLY	GLY	(chain A and (resid -1 through 8 or resid 10...	A	A	65 - 72	73 - 80
1	5	HIS	HIS	HIS	HIS	(chain A and (resid -1 through 8 or resid 10...	A	A	0	8
1	6	HIS	HIS	ALA	ALA	(chain A and (resid -1 through 8 or resid 10...	A	A	-1 - 394	7 - 402
1	7	ILE	ILE	GLN	GLN	(chain A and (resid -1 through 8 or resid 10...	A	A	151 - 152	159 - 160
1	8	TYR	TYR	GLN	GLN	(chain A and (resid -1 through 8 or resid 10...	A	A	154 - 263	162 - 271
1	9	ARG	ARG	ARG	ARG	(chain A and (resid -1 through 8 or resid 10...	A	A	264 - 266	272 - 274
1	10	HIS	HIS	ALA	ALA	(chain A and (resid -1 through 8 or resid 10...	A	A	-1 - 394	7 - 402
1	11	HIS	HIS	ALA	ALA	(chain A and (resid -1 through 8 or resid 10...	A	A	-1 - 394	7 - 402
1	12	HIS	HIS	ALA	ALA	(chain A and (resid -1 through 8 or resid 10...	A	A	-1 - 394	7 - 402
1	13	HIS	HIS	ALA	ALA	(chain A and (resid -1 through 8 or resid 10...	A	A	-1 - 394	7 - 402
2	1	HIS	HIS	GLU	GLU	(chain B and (resid -1 through 8 or resid 10...	B	B	-1 - 8	7 - 16
2	2	GLY	GLY	ALA	ALA	(chain B and (resid -1 through 8 or resid 10...	B	B	10 - 61	18 - 69
2	3	THR	THR	THR	THR	(chain B and (resid -1 through 8 or resid 10...	B	B	63	71
2	4	GLY	GLY	GLY	GLY	(chain B and (resid -1 through 8 or resid 10...	B	B	65 - 72	73 - 80
2	5	GLY	GLY	GLY	GLY	(chain B and (resid -1 through 8 or resid 10...	B	B	75	83
2	6	HIS	HIS	ALA	ALA	(chain B and (resid -1 through 8 or resid 10...	B	B	82 - 94	90 - 102
2	7	GLU	GLU	GLU	GLU	(chain B and (resid -1 through 8 or resid 10...	B	B	95	103
2	8	HIS	HIS	GLU	GLU	(chain B and (resid -1 through 8 or resid 10...	B	B	-1 - 391	7 - 399
2	9	HIS	HIS	GLU	GLU	(chain B and (resid -1 through 8 or resid 10...	B	B	-1 - 391	7 - 399
2	10	HIS	HIS	GLU	GLU	(chain B and (resid -1 through 8 or resid 10...	B	B	-1 - 391	7 - 399
2	11	HIS	HIS	GLU	GLU	(chain B and (resid -1 through 8 or resid 10...	B	B	-1 - 391	7 - 399

#1: Protein	8-amino-7-oxononanoate synthase / AONS / 7-keto-8-amino-pelargonic acid synthase / KAPA synthase / 8-amino-7-ketopelargonate synthase Mass: 42827.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria) Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: bioF, Bphy_0172 / Variant: STM815 / Production host: Escherichia coli (E. coli) References: UniProt: B2JKH6, 8-amino-7-oxononanoate synthase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

8-amino-7-oxononanoate synthase / AONS / 7-keto-8-amino-pelargonic acid synthase / KAPA synthase / 8-amino-7-ketopelargonate synthase

Mass: 42827.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria)
Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: bioF, Bphy_0172 / Variant: STM815 / Production host:

Escherichia coli (E. coli)
References: UniProt: B2JKH6, 8-amino-7-oxononanoate synthase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.67 Å³/Da / Density % sol: 53.93 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: SEC purified BuphA.00096.a.B1.PW38412 at 8.864mg/ml (in 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol , 2 mM DTT, 0.025% Azide ) was crystallized by sitting drop vapor diffusion at 14C with ...Details: SEC purified BuphA.00096.a.B1.PW38412 at 8.864mg/ml (in 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol , 2 mM DTT, 0.025% Azide ) was crystallized by sitting drop vapor diffusion at 14C with an equal volume of protein:mother liquor (Morpheus E3: 0.03M Diethylene glycol, 0.03M Triethylene glycol, 0.03M Tetraethylene glycol, 0.03M Pentaethylene glycol, 0.1M Imidazole/MES buffer pH 6.5, 20% Glycerol, 10% PEG4000), then flash-frozen for data collection. Crystal ID 299435e3 data set aas7-2

Crystal

Density Matthews: 2.67 Å³/Da / Density % sol: 53.93 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: SEC purified BuphA.00096.a.B1.PW38412 at 8.864mg/ml (in 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol , 2 mM DTT, 0.025% Azide ) was crystallized by sitting drop vapor diffusion at 14C with ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 6, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.8→39.9 Å / Num. obs: 84896 / % possible obs: 99.2 % / Redundancy: 5.345 % / B_iso Wilson estimate: 29.193 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.068 / R_rim(I) all: 0.075 / Χ²: 1.018 / Net I/σ(I): 15.99 / Num. measured all: 453780 / Scaling rejects: 10

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.8-1.85	5.371	0.565	3.06	33783	6304	6290	0.84	0.624	99.8
1.85-1.9	5.39	0.478	3.58	32701	6089	6067	0.886	0.528	99.6
1.9-1.95	5.362	0.38	4.63	31561	5920	5886	0.925	0.42	99.4
1.95-2.01	5.389	0.291	5.88	30934	5773	5740	0.954	0.322	99.4
2.01-2.08	5.385	0.242	7.18	29825	5586	5539	0.967	0.268	99.2
2.08-2.15	5.404	0.184	9.16	28949	5417	5357	0.981	0.203	98.9
2.15-2.23	5.403	0.15	11.2	27895	5242	5163	0.985	0.166	98.5
2.23-2.32	5.323	0.127	12.91	26427	5042	4965	0.989	0.14	98.5
2.32-2.43	5.373	0.106	14.91	25700	4848	4783	0.992	0.118	98.7
2.43-2.55	5.351	0.091	16.86	24433	4635	4566	0.994	0.1	98.5
2.55-2.68	5.35	0.08	19.06	23298	4416	4355	0.996	0.088	98.6
2.68-2.85	5.351	0.068	21.85	22146	4181	4139	0.996	0.075	99
2.85-3.04	5.341	0.056	25.31	20888	3951	3911	0.997	0.062	99
3.04-3.29	5.333	0.048	29.15	19613	3694	3678	0.998	0.053	99.6
3.29-3.6	5.301	0.042	32.09	17879	3384	3373	0.998	0.047	99.7
3.6-4.02	5.293	0.039	35.02	16365	3101	3092	0.998	0.043	99.7
4.02-4.65	5.309	0.034	37.34	14589	2754	2748	0.999	0.037	99.8
4.65-5.69	5.26	0.032	37.58	12272	2336	2333	0.999	0.036	99.9
5.69-8.05	5.141	0.032	37.14	9490	1849	1846	0.997	0.035	99.8
8.05-39.9	4.725	0.031	38.47	5032	1084	1065	0.999	0.035	98.2

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Processing

Software

Name	Version	Classification
PHENIX	dev_3409	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5JAY

5jay

Resolution: 1.8→39.9 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1936	4934	6.02 %
R_work	0.1642	76983	-
obs	0.1659	81917	95.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 94.99 Å² / B_iso mean: 28.1894 Å² / B_iso min: 9.72 Å²

Refinement step

Cycle: final / Resolution: 1.8→39.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5706	0	0	713	6419
B_iso mean	-	-	-	37.12	-
Num. residues	-	-	-	-	783

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	3166	X-RAY DIFFRACTION	4.283	TORSIONAL
1	2	B	3166	X-RAY DIFFRACTION	4.283	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8-1.8204	0.2909	130	0.2363	2417	2547	90
1.8204-1.8418	0.2637	164	0.2208	2365	2529	90
1.8418-1.8643	0.2138	148	0.2137	2407	2555	90
1.8643-1.8879	0.1956	128	0.2067	2410	2538	91
1.8879-1.9127	0.2237	190	0.1993	2372	2562	91
1.9127-1.9389	0.2369	172	0.1965	2421	2593	92
1.9389-1.9666	0.2491	162	0.1931	2504	2666	94
1.9666-1.996	0.237	149	0.1793	2515	2664	94
1.996-2.0272	0.218	168	0.1803	2515	2683	95
2.0272-2.0604	0.22	162	0.1786	2489	2651	94
2.0604-2.0959	0.2108	163	0.1762	2533	2696	95
2.0959-2.1341	0.2065	140	0.1715	2568	2708	96
2.1341-2.1751	0.2084	160	0.1681	2552	2712	96
2.1751-2.2195	0.2035	169	0.1706	2528	2697	96
2.2195-2.2678	0.2273	173	0.1653	2508	2681	94
2.2678-2.3205	0.1963	169	0.162	2542	2711	96
2.3205-2.3785	0.1711	171	0.1645	2567	2738	96
2.3785-2.4428	0.2251	165	0.1666	2590	2755	97
2.4428-2.5147	0.2083	152	0.1654	2594	2746	97
2.5147-2.5958	0.1891	176	0.1621	2591	2767	97
2.5958-2.6886	0.2063	166	0.1733	2642	2808	98
2.6886-2.7962	0.1994	155	0.1701	2647	2802	98
2.7962-2.9235	0.2111	179	0.1696	2615	2794	98
2.9235-3.0775	0.2069	190	0.1635	2628	2818	98
3.0775-3.2703	0.1716	146	0.1564	2701	2847	99
3.2703-3.5226	0.1834	183	0.1557	2684	2867	99
3.5226-3.8769	0.1873	177	0.1496	2716	2893	100
3.8769-4.4372	0.1489	179	0.1348	2711	2890	100
4.4372-5.588	0.1592	175	0.1446	2765	2940	100
5.588-39.9096	0.1794	173	0.1667	2886	3059	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	4.4813	3.5889	-2.4358	3.0623	-1.859	1.367	-0.3311	0.0714	-0.2495	-0.5212	0.1119	-0.362	0.2761	0.1863	0.1269	0.285	0.0053	0.0648	0.2906	-0.0045	0.3067	22.9278	-11.4377	-19.6484
2	0.9962	-0.1386	0.3589	0.7022	0.046	0.5095	-0.0665	-0.0581	0.0597	0.0419	0.0326	0.0542	-0.0888	-0.0311	0.0386	0.1251	-0	0.0166	0.1373	0.0106	0.1088	12.0227	-6.2794	7.3149
3	1.1169	-0.1361	0.1988	0.8178	0.2655	0.5804	-0.0153	-0.0449	-0.0688	0.0282	0.0297	-0.03	-0.0151	0.0427	-0.0181	0.1144	-0.0036	0.0067	0.1235	0.0253	0.1013	22.9382	-16.1227	7.4299
4	6.7576	-1.5203	3.2817	1.4963	-0.2487	1.8009	-0.4576	-0.5084	0.7034	0.4098	0.2259	-0.4376	-0.4153	-0.1168	0.1171	0.3338	0.0268	-0.0757	0.286	-0.0733	0.4026	18.056	11.7923	17.6634
5	1.4153	0.1295	-0.1997	2.481	0.3457	2.4496	-0.076	-0.0993	0.0647	0.0163	0.1164	-0.0332	-0.0378	-0.0876	0.0074	0.0476	0.0115	0.008	0.1405	-0.0045	0.1223	2.5408	2.6527	-1.2919
6	2.7081	1.0454	-0.2795	1.591	0.0658	1.3514	0.0473	0.0118	0.049	0.0242	0.0361	-0.1637	-0.2376	0.2313	-0.0507	0.2017	-0.0355	0.0084	0.1398	-0.0035	0.1058	24.3005	8.6234	-14.9763
7	2.8037	0.308	-0.6433	1.4359	0.1293	1.4072	-0.0227	0.1235	0.0479	-0.0867	0.0623	0.0134	-0.1244	-0.0121	-0.0654	0.1503	-0.0131	-0.0017	0.112	0.0129	0.0625	16.3313	5.858	-17.466
8	2.3279	0.1687	-1.1956	0.6858	0.5561	1.2274	-0.0332	-0.1279	-0.2097	0.0447	-0.1657	-0.2764	0.1319	0.4068	0.191	0.1354	-0.0142	-0.0107	0.1926	0.0423	0.2089	8.8379	-2.4907	-8.9926
9	1.7007	-0.323	-0.3153	1.6115	1.4419	3.5852	-0.0503	-0.2972	0.5935	-0.0746	0.22	-0.1947	-0.4692	0.3621	-0.16	0.2908	0.0552	-0.0054	0.2128	-0.0743	0.4043	7.6428	26.2642	-0.1159

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 32 )	A	-1 - 32
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 133 )	A	33 - 133
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 134 through 394 )	A	134 - 394
4	X-RAY DIFFRACTION	4	chain 'B' and (resid -1 through 32 )	B	-1 - 32
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 33 through 83 )	B	33 - 83
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 84 through 201 )	B	84 - 201
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 202 through 264 )	B	202 - 264
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 265 through 291 )	B	265 - 291
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 292 through 391 )	B	292 - 391

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About Yorodumi

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Yorodumi