PDB-3bjd: Crystal structure of putative 3-oxoacyl-(acyl-carrier-protein) sy...

ID or keywords:

Entry

Database: PDB / ID: 3bjd

Title

Crystal structure of putative 3-oxoacyl-(acyl-carrier-protein) synthase from Pseudomonas aeruginosa

Components

Putative 3-oxoacyl-(acyl-carrier-protein) synthase

Keywords

TRANSFERASE /

structural genomics / APC5632 / 3-oxoacyl-(acyl-carrier-protein) synthase / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

hydrolase activity, hydrolyzing O-glycosyl compounds /

periplasmic space
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Osipiuk, J. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of putative 3-oxoacyl-(acyl-carrier-protein) synthase from Pseudomonas aeruginosa.
Authors: Osipiuk, J. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.

History

Deposition	Dec 3, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bjd.cif.gz	233.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3bjd.ent.gz	198.6 KB	Display	PDB format
PDBx/mmJSON format	3bjd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bj/3bjd ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bjd	HTTPS FTP

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Related structure data

Similar structure data	4o90-d 4rzv-d 5kvu-1 4xl2-d 4li5-2 2yp1-2 1s0a-d 1j1w-2 4wya-2 2bwp-1 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
Other databases	TargetDB: APC5632

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative 3-oxoacyl-(acyl-carrier-protein) synthase

B: Putative 3-oxoacyl-(acyl-carrier-protein) synthase

C: Putative 3-oxoacyl-(acyl-carrier-protein) synthase

hetero molecules

115 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative 3-oxoacyl-(acyl-carrier-protein) synthase

B: Putative 3-oxoacyl-(acyl-carrier-protein) synthase

hetero molecules

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

2

C: Putative 3-oxoacyl-(acyl-carrier-protein) synthase

hetero molecules

C: Putative 3-oxoacyl-(acyl-carrier-protein) synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	97.566, 156.904, 136.022
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-807- HOH
2	1	C-809- HOH

Details

AUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

#1: Protein	Putative 3-oxoacyl-(acyl-carrier-protein) synthase Mass: 38141.211 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3518 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HY91
#2: Chemical	ChemComp-NI / NICKEL (II) ION / Nickel Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 938 / 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: 2.27 Å³/Da / Density % sol: 45.93 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.2 M Magnesium chloride, 30% PEG 4000, 0.1 M Sodium cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
Detector	Type: SBC-3 / Detector: CCD / Date: Apr 3, 2005
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.85→39.9 Å / Num. all: 87637 / Num. obs: 87637 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / B_iso Wilson estimate: 32.2 Å² / R_merge(I) obs: 0.079 / Χ²: 1.56 / Net I/σ(I): 12.9
Reflection shell	Resolution: 1.85→1.9 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.552 / Mean I/σ(I) obs: 2.04 / Num. unique all: 6183 / Χ²: 0.979 / % possible all: 84.8

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-2000		data reduction
SHELXD		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.85→39.9 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.941 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2033	2644	3 %	RANDOM
R_work	0.1612	-	-	-
all	0.1625	87586	-	-
obs	0.1625	87586	98.66 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 21.677 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.01 Å²	0 Å²	0 Å²
2-	-	0.72 Å²	0 Å²
3-	-	-	0.28 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→39.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7828	0	31	938	8797

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	8509
X-RAY DIFFRACTION	r_angle_refined_deg	1.363	1.95	11610
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.658	5	1097
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.632	22.979	480
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.69	15	1489
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.928	15	106
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	1257
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6716
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	4214
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	5858
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	732
X-RAY DIFFRACTION	r_metal_ion_refined	0.083	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.2	0.2	108
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.137	0.2	55
X-RAY DIFFRACTION	r_mcbond_it	0.938	1.5	5237
X-RAY DIFFRACTION	r_mcangle_it	1.339	2	8130
X-RAY DIFFRACTION	r_scbond_it	2.371	3	3748
X-RAY DIFFRACTION	r_scangle_it	3.559	4.5	3408

LS refinement shell

Resolution: 1.85→1.9 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.295	159	-
R_work	0.243	5227	-
all	-	5386	-
obs	-	5386	83.43 %

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	1.9396	1.176	-2.2336	3.6935	-2.9496	10.2339	-0.0551	-0.1908	0.0221	-0.1247	-0.1549	-0.2977	0.1461	0.6347	0.21	-0.0192	0.0114	-0.0227	0.0612	-0.0123	0.0393	34.8203	40.8903	21.2647
2	1.5098	0.4288	-0.8407	2.9483	1.4711	1.5025	0.0351	-0.1434	-0.2168	-0.0141	-0.02	-0.0702	0.0607	-0.0041	-0.0151	0.0434	-0.0044	-0.0174	0.0165	0.0199	0.0266	21.8353	33.6019	21.3281
3	2.9556	-0.9868	-2.5487	0.6912	0.5425	5.8487	0.0851	-0.0574	0.1117	0.0781	0.0356	-0.0734	-0.2269	-0.0376	-0.1207	0.0571	-0.0136	0.0203	0.0314	-0.0324	-0.0067	22.1139	48.6562	32.4265
4	1.177	-0.5764	-0.572	0.8737	0.7065	0.7235	0.1527	0.0383	0.0464	-0.1025	-0.0965	0.0091	-0.0861	-0.1263	-0.0561	0.033	0.0081	0.0212	0.057	0.001	0.0242	15.8609	52.0171	18.0912
5	50.2319	0.3547	13.5638	0.0025	0.0958	3.6626	0.0746	-1.2828	2.3083	0.7184	-0.9702	0.383	-1.2113	0.1554	0.8957	0.346	0.0374	-0.0004	0.2968	0.0199	0.317	19.1554	74.4994	21.7254
6	0.5954	0.2195	0.5175	0.0837	0.1738	0.5506	0.0451	-0.0127	0.0647	-0.0369	0.0232	0.008	-0.1119	-0.002	-0.0683	0.0604	-0.0221	0.0461	0.0187	-0.0156	0.0597	33.6022	62.5165	9.8898
7	1.0884	-0.004	-0.1042	0.158	0.0274	0.2993	0.1001	-0.008	0.0602	-0.0311	0.0041	0.015	-0.0548	-0.0324	-0.1043	0.0357	0.0031	0.0261	0.0255	-0.0132	0.049	23.1006	57.1718	16.7322
8	34.7402	17.0502	3.5704	8.3681	1.7523	0.367	-1.0446	0.0766	-0.5409	-1.134	1.1818	-0.2068	-1.2516	-0.202	-0.1372	0.2174	-0.0091	0.0712	0.1915	-0.0239	0.2071	27.884	73.5356	12.0686
9	8.0339	4.043	2.137	3.7623	1.5719	2.7265	-0.2957	-0.0173	0.5452	-0.2869	0.1279	0.2017	-0.3046	-0.0523	0.1677	0.0703	-0.0403	0.0125	-0.0261	0.0027	0.0529	40.1946	74.352	9.5906
10	1.4602	-0.7078	2.4944	2.3725	-0.4328	5.6558	0.0208	0.0226	0.3075	-0.1069	-0.0371	-0.1103	-0.4298	-0.0483	0.0163	0.0096	0.054	0.0481	0.0096	0.0207	0.082	11.8455	65.6519	10.8194
11	10.9844	4.9437	2.372	2.3264	0.9952	0.8193	0.2106	-0.3003	0.2568	0.0818	-0.1166	0.1971	-0.0319	-0.0139	-0.094	0.0442	-0.0352	0.0521	0.0109	-0.0882	0.0283	31.5	66.1085	28.1757
12	1.5677	-0.664	-0.2104	0.4396	-0.3718	1.3699	-0.0035	0.1048	-0.054	0.102	0.0664	0.1563	-0.0465	-0.144	-0.0629	0.0055	-0.0117	0.0046	0.0548	-0.0033	0.0288	1.741	37.9732	5.743
13	0.1417	-0.3854	-0.3034	1.6736	0.5423	0.7769	-0.0016	0.0488	-0.003	0.0388	0.0032	0.0258	0.0478	-0.0301	-0.0016	0.0108	-0.0063	0.0011	0.0465	0.0056	0.0325	11.2694	32.8168	1.1403
14	5.0687	0.8966	-2.5878	0.9081	-0.5086	2.1476	-0.1249	0.0345	-0.2438	-0.0661	0.0506	-0.06	0.0935	0.1582	0.0743	-0.0019	0.0097	-0.0041	0.0409	-0.0391	0.0032	36.4916	29.9485	-9.953
15	17.7093	-5.2611	11.7861	3.7928	-2.3174	8.4726	-0.0159	-0.0447	0.0542	-0.1103	-0.1167	-0.3069	-0.1368	-0.1657	0.1326	-0.0012	-0.0142	0.0052	0.1146	0.0092	-0.0495	30.1562	34.8615	-21.1485
16	0.0397	0.1228	0.2995	0.38	0.9267	2.2602	0.0176	0.0771	0.1322	-0.0292	-0.0604	-0.0318	-0.2477	-0.0592	0.0428	0.0254	0.0386	0.0059	0.1145	0.0625	0.0027	12.791	45.735	-21.4067
17	1.2465	-0.2333	0.6912	0.0798	-0.0303	1.1761	0.012	0.0429	0.0313	-0.0421	0.0619	-0.027	-0.1769	-0.0112	-0.0739	0.0539	-0.0025	0.0192	0.0227	0.0363	0.0313	20.4848	55.8772	-9.4676
18	0.784	-0.3775	-0.3037	0.2557	0.2753	0.3426	0.0257	0.0141	0.0239	-0.0235	0.0242	-0.0798	-0.0306	-0.0504	-0.0499	0.016	0.0054	0.0021	0.0709	0.015	0.0266	19.0207	41.5999	-8.8165
19	7.1026	-8.4387	-2.0793	20.4578	3.9932	3.1012	0.1545	0.0218	0.0906	-1.0385	0.1941	-0.1531	-0.5198	0.2261	-0.3486	0.1072	-0.0412	0.0101	0.0574	0.0875	-0.1064	16.9831	55.5717	-29.8274
20	2.1076	-0.0246	2.9219	1.3064	-1.1457	4.9969	0.0743	1.0559	0.239	-0.0102	-0.0478	-0.1922	0.0569	0.8969	-0.0265	0.0903	-0.0067	0.0617	0.2785	0.027	-0.0216	28.6709	53.1282	-19.8506
21	2.8685	0.542	-0.422	2.7593	0.1522	0.1538	-0.0155	-0.0083	0.0343	0.0043	0.1393	-0.1197	-0.0719	0.0692	-0.1237	-0.0017	-0.0004	0.0076	0.0859	-0.0265	0.0168	36.5104	38.5573	-6.3449
22	6.5361	-1.5386	4.7922	0.4002	-1.3847	5.2439	0.033	0.0871	-0.1301	-0.0023	0.0139	-0.0958	0.0909	-0.107	-0.0469	0.0069	-0.0143	-0.0071	0.0751	0.0009	-0.0029	14.5705	35.1783	-20.695
23	14.1633	-4.9848	4.1632	3.0486	-2.0222	4.111	-0.1065	0.1226	0.5329	0.135	-0.036	-0.469	-0.4904	0.1884	0.1425	0.047	-0.0941	-0.0232	-0.0255	-0.0029	0.0856	36.6312	18.6104	8.7738
24	0.6012	0.0822	-0.0655	0.6168	-0.2847	1.4922	0.1026	-0.0605	0.0057	0.0097	-0.1202	-0.1599	-0.0594	0.1687	0.0176	-0.0316	-0.0487	-0.019	0.0616	0.0162	0.1013	40.3847	7.3613	9.6756
25	0.0119	0.1961	0.0399	3.3099	0.4567	0.7142	0.0558	0.1184	-0.0131	0.5361	-0.1486	0.3745	0.1581	0.0501	0.0928	0.0539	-0.0326	0.0329	-0.0138	0.0023	0.0198	21.1497	-8.3178	25.6683
26	1.3926	-2.0037	-0.0989	4.7947	4.6566	10.6665	-0.1583	0.0625	-0.0209	0.3557	0.1017	0.0625	-0.2255	-0.2658	0.0566	0.1288	0.0048	0.0468	-0.0676	-0.0126	0.031	13.5599	17.4449	24.7512
27	0.3109	-0.1914	0.0917	1.0976	0.685	0.7706	0.0583	-0.0093	-0.0183	0.0101	-0.0928	0.0551	-0.008	0.0139	0.0345	0.0065	-0.0138	0.0002	0.0141	-0.0102	0.0779	15.8849	0.1121	5.4009
28	0.265	-0.3657	0.5043	1.0979	0.0471	1.8901	-0.0121	0.1915	-0.0465	0.1213	-0.0047	0.1282	-0.2342	-0.0071	0.0167	0.0453	-0.0167	0.0367	-0.0396	-0.0281	0.0878	13.0025	16.9949	11.7766
29	0.1918	0.5659	0.3945	2.2718	0.8108	1.0184	0.0707	-0.0917	-0.007	-0.0161	-0.1753	0.0946	-0.0312	0.0211	0.1046	0.0178	-0.022	-0.0123	0.0155	-0.0158	0.072	23.3521	-0.8808	15.6697
30	8.3744	-0.6607	-3.9914	4.6015	-8.7046	26.9107	0.3753	-1.9325	-1.0468	2.3863	0.1367	1.1368	0.4798	-0.3311	-0.512	0.3011	-0.0365	0.0684	0.3125	-0.1907	0.3222	2.2186	11.05	24.6933
31	1.0866	1.1154	0.304	10.7909	-1.7927	0.5443	0.073	-0.1237	0.0411	0.5275	-0.1648	0.5482	0.0171	-0.0473	0.0918	0.0223	-0.0472	0.111	0.0408	-0.0538	0.0765	3.2978	5.6454	16.987
32	0.5843	0.3856	0.1588	1.0683	0.2972	0.2912	0.0541	0.0153	0.0026	0.0664	-0.0809	0.0503	0.0601	0.0199	0.0268	0.0306	-0.0106	0.0058	0.0195	-0.0028	0.065	19.8544	-12.9573	15.4207
33	3.8947	-4.7989	-1.6036	6.8263	3.2557	2.4535	-0.2352	-0.1883	-0.1782	0.5242	0.1594	0.0845	0.007	0.2702	0.0758	0.1171	-0.06	0.0105	0.0081	-0.0187	-0.0164	21.799	9.2259	29.7025

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 19	4 - 21
2	X-RAY DIFFRACTION	2	A	A	20 - 45	22 - 47
3	X-RAY DIFFRACTION	3	A	A	46 - 62	48 - 64
4	X-RAY DIFFRACTION	4	A	A	63 - 108	65 - 110
5	X-RAY DIFFRACTION	5	A	A	109 - 127	111 - 129
6	X-RAY DIFFRACTION	6	A	A	128 - 208	130 - 210
7	X-RAY DIFFRACTION	7	A	A	209 - 242	211 - 244
8	X-RAY DIFFRACTION	8	A	A	243 - 253	245 - 255
9	X-RAY DIFFRACTION	9	A	A	254 - 276	256 - 278
10	X-RAY DIFFRACTION	10	A	A	277 - 310	279 - 312
11	X-RAY DIFFRACTION	11	A	A	311 - 327	313 - 329
12	X-RAY DIFFRACTION	12	B	B	2 - 35	4 - 37
13	X-RAY DIFFRACTION	13	B	B	36 - 91	38 - 93
14	X-RAY DIFFRACTION	14	B	B	92 - 110	94 - 112
15	X-RAY DIFFRACTION	15	B	B	111 - 122	113 - 124
16	X-RAY DIFFRACTION	16	B	B	123 - 159	125 - 161
17	X-RAY DIFFRACTION	17	B	B	160 - 206	162 - 208
18	X-RAY DIFFRACTION	18	B	B	207 - 246	209 - 248
19	X-RAY DIFFRACTION	19	B	B	251 - 268	253 - 270
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