PDB-4a0s: STRUCTURE OF THE 2-OCTENOYL-COA CARBOXYLASE REDUCTASE CINF IN COM...

ID or keywords:

Entry

Database: PDB / ID: 4a0s

Title

STRUCTURE OF THE 2-OCTENOYL-COA CARBOXYLASE REDUCTASE CINF IN COMPLEX WITH NADP AND 2-OCTENOYL-COA

Components

OCTENOYL-COA REDUCTASE/CARBOXYLASE

Keywords

OXIDOREDUCTASE / TRANSFERASE / CINNABARAMIDE PKS BIOSYNTHESIS

Function / homology

Function and homology information

crotonyl-CoA reductase activity / nucleotide binding / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function

Biological species

STREPTOMYCES SP. (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Quade, N. / Huo, L. / Rachid, S. / Heinz, D.W. / Muller, R.

Citation

Journal: Nat. Chem. Biol. / Year: 2011
Title: Unusual carbon fixation gives rise to diverse polyketide extender units.
Authors: Quade, N. / Huo, L. / Rachid, S. / Heinz, D.W. / Muller, R.

History

Deposition	Sep 12, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 7, 2011	Provider: repository / Type: Initial release
Revision 1.1	Dec 28, 2011	Group: Other
Revision 1.2	Jan 16, 2019	Group: Data collection / Database references / Derived calculations Category: citation / pdbx_struct_assembly / pdbx_struct_assembly_prop Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4a0s.cif.gz	697.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4a0s.ent.gz	579.8 KB	Display	PDB format
PDBx/mmJSON format	4a0s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4a0s_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	4a0s_full_validation.pdf.gz	2.4 MB	Display
Data in XML	4a0s_validation.xml.gz	43 KB	Display
Data in CIF	4a0s_validation.cif.gz	71.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a0/4a0s ftp://data.pdbj.org/pub/pdb/validation_reports/a0/4a0s	HTTPS FTP

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Related structure data

Related structure data	4a10C 3krtS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4a10-d 3m6i-1 6t2c-d 2cdc-d 4jbi-2 3qe3-1 3pii-d 4w6z-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
Related items in Molecule of the Month	#13 - Jan 2001 Alcohol Dehydrogenase similarity (7) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: OCTENOYL-COA REDUCTASE/CARBOXYLASE

B: OCTENOYL-COA REDUCTASE/CARBOXYLASE

C: OCTENOYL-COA REDUCTASE/CARBOXYLASE

D: OCTENOYL-COA REDUCTASE/CARBOXYLASE

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	96.010, 83.300, 122.740
Angle α, β, γ (deg.)	90.00, 110.96, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	OCTENOYL-COA REDUCTASE/CARBOXYLASE / CINF / 2-OCTENOYL-COA CARBOXYLASE/REDUCTASE Mass: 48030.520 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-448 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES SP. (bacteria) / Strain: JS360 / Plasmid: PSTW42 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F0V3Z3
#2: Chemical	ChemComp-CO8 / OCTANOYL-COENZYME A Mass: 893.730 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₉H₅₀N₇O₁₇P₃S
#3: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1892 / 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: 2.39 Å³/Da / Density % sol: 48 % / Description: NONE
Crystal grow	pH: 7 / Details: 0.1 M TRIS PH 7, 20% GLYCEROL, 12% PEG 8000.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 4, 2010 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.9→47.2 Å / Num. obs: 140724 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / R_merge(I) obs: 0.01 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.04 / Mean I/σ(I) obs: 3.6 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KRT

3krt

Resolution: 1.9→47.21 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.908 / SU B: 8.423 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25042	7037	5 %	RANDOM
R_work	0.19916	-	-	-
obs	0.20171	133687	100 %	-

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: 21.788 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2 Å²	0 Å²	-0.25 Å²
2-	-	-0.03 Å²	0 Å²
3-	-	-	0.05 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→47.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13406	0	420	1892	15718

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	14177
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.634	1.991	19319
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.954	5	1787
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.658	23.13	591
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.587	15	2211
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.077	15	123
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	2175
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	10711
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.343	1.5	8815
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.677	2	14108
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.389	3	5362
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.385	4.5	5204
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.332	465	-
R_work	0.277	8832	-
obs	-	-	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	1.4866	-0.5985	-0.5748	1.551	0.1815	3.7174	0.0112	0.2494	0.2187	-0.2422	-0.0334	-0.2961	0.202	0.1446	0.0223	0.1898	-0.0286	0.0414	0.139	0.065	0.2394	40.995	19.578	6.287
2	0.6611	-0.2546	0.0154	1.0873	-0.0894	0.5274	-0.045	-0.0752	0.1702	0.0916	0.0276	-0.1902	-0.091	0.0524	0.0175	0.1746	-0.0174	-0.0133	0.1416	0.0002	0.2106	36.614	20.039	22.754
3	0.581	0.0291	-0.1208	0.4469	-0.0765	0.2463	0.0071	-0.0013	0.0931	-0.0122	0.0151	0.0257	-0.0387	-0.014	-0.0221	0.1862	-0.0014	-0.0066	0.1474	0.0122	0.1878	18.817	16.789	20.495
4	4.0271	-0.6901	-0.821	3.4281	0.3771	1.5385	-0.0107	-0.153	0.271	0.1143	0.0337	0.0653	-0.1744	-0.0684	-0.0231	0.239	0.0261	0.0487	0.124	-0.0603	0.1938	6.552	32.16	41.671
5	0.3731	0.0426	-0.0483	0.4558	-0.1031	0.2539	0.0034	-0.0172	0.1182	0.0341	0.0033	0.0332	-0.0631	-0.04	-0.0066	0.1964	0.0008	-0.0045	0.1549	0.0028	0.2144	14.318	21.68	25.407
6	1.8809	0.756	0.9692	8.4388	6.9155	8.9227	0.0848	0.153	0.1989	-0.2317	0.0723	-0.0635	-0.103	-0.1795	-0.1571	0.1958	0.0059	-0.0194	0.1737	0.0788	0.2384	12.48	28.414	8.623
7	1.5184	0.0289	-0.1968	1.9093	0.4105	1.9904	-0.04	-0.1866	-0.0754	-0.0094	-0.083	-0.2654	0.0395	0.2149	0.1231	0.143	0.0117	-0.0071	0.1923	0.0165	0.2486	52.147	-16.836	26.371
8	0.5667	0.1179	-0.0617	0.9701	-0.3167	0.7725	-0.0649	0.1021	-0.1098	-0.2774	0.0482	0.006	0.2117	-0.0565	0.0166	0.2232	-0.0148	0.0095	0.1367	-0.0215	0.1724	33.211	-21.225	14.333
9	0.5848	-0.0835	-0.1656	0.3604	-0.0109	0.3287	-0.024	-0.0179	-0.0648	0.0052	0.0164	0.0016	0.0455	-0.0187	0.0075	0.1896	-0.0015	-0.0004	0.1542	0.0114	0.1819	23.435	-16.542	29.933
10	4.3176	-0.0484	0.5565	1.4224	1.2787	1.2496	-0.1497	0.0617	-0.2748	0.0668	0.0226	0.1598	0.0799	-0.0056	0.127	0.2736	-0.0768	-0.0268	0.0821	-0.0132	0.2354	2.141	-33.398	24.518
11	0.3905	-0.1963	-0.0275	0.4821	-0.0739	0.3057	-0.0266	-0.0332	-0.1049	-0.0365	0.0206	0.0733	0.0806	-0.0491	0.006	0.2082	-0.0157	0.0014	0.1549	0.0134	0.2103	14.777	-22.121	29.673
12	4.8569	4.2412	4.1288	8.8815	5.6235	8.3122	0.0378	-0.1918	-0.3048	0.272	0.1257	-0.2582	0.1636	0.0191	-0.1634	0.2221	0.0464	0.0373	0.1853	0.0719	0.2292	27.63	-28.397	42.429
13	0.8957	-0.0705	-0.3543	0.497	-0.0902	1.6755	0.0007	-0.0085	0.0848	-0.0154	-0.0611	0.0743	0.1103	-0.2566	0.0603	0.1042	0.0031	-0.0209	0.2341	-0.0156	0.1847	-33.997	-5.088	22.038
14	0.8633	0.2778	0.1786	0.4097	-0.3304	1.2409	-0.0083	0.0541	-0.0493	-0.0643	-0.0239	-0.0346	0.2656	0.0104	0.0323	0.148	0.0017	-0.0032	0.2385	-0.0204	0.1868	-24.976	-9.267	26.226
15	0.6285	0.07	-0.1303	0.1803	0.0985	0.276	-0.0216	0.0453	0.0513	-0.027	-0.0154	0.038	-0.0089	-0.067	0.0371	0.1508	0.0009	-0.0173	0.2003	0.0132	0.1723	-14.795	0.821	23.172
16	5.3492	-1.9527	-1.4797	9.3357	-3.776	2.5858	0.3259	0.2857	-0.5101	-0.982	-0.0799	0.9719	0.3577	-0.0699	-0.2459	0.2959	-0.0395	-0.1361	0.2161	-0.0629	0.1452	-1.843	-15.48	1.477
17	0.9224	-0.0227	0.0464	0.7822	-0.4204	0.8904	0.0215	0.1851	-0.0731	-0.2132	0.0151	0.0245	0.2032	0.0025	-0.0366	0.2002	-0.0092	-0.0257	0.1735	-0.0161	0.1487	4.79	-10.82	10.74
18	0.782	0.0679	0.1079	0.3764	0.1136	0.3744	-0.0308	0.1561	0.1604	-0.0717	-0.0189	0.0602	-0.0641	-0.0975	0.0498	0.1265	0.011	-0.0194	0.2319	0.0419	0.1751	-18.486	5.768	14.812
19	2.025	0.4628	0.666	0.8153	0.1206	0.6017	-0.1135	-0.3659	0.1677	-0.0285	-0.0498	0.1291	-0.0165	-0.3094	0.1633	0.1529	-0.0152	0.01	0.3467	-0.0491	0.1079	-13.321	4.575	67.694
20	0.9944	-0.2195	0.4321	0.266	-0.2526	1.615	-0.1021	-0.1753	0.2824	0.0747	-0.0554	-0.0095	-0.2001	-0.0276	0.1574	0.1601	-0.0065	-0.0003	0.2564	-0.0613	0.1735	-10.508	9.31	59.5
21	0.8065	0.013	-0.015	0.2793	0.125	0.5033	-0.0105	-0.1532	0.0492	0.0486	-0.024	0.0205	0.0303	-0.0635	0.0345	0.1728	-0.0027	0.0046	0.2314	0.0031	0.1474	-1.25	-0.593	53.053
22	4.5987	-0.6092	-1.6573	13.5323	-0.9591	1.705	0.3377	-0.2653	0.3203	1.0548	-0.1519	0.4908	-0.1321	0.0807	-0.1859	0.2548	-0.0756	0.0294	0.2872	-0.1012	0.0825	24.026	16.953	56.625
23	0.4833	0.0833	-0.1423	0.2394	-0.1143	0.5589	-0.0049	-0.1469	0.0381	0.0494	-0.0152	-0.051	-0.104	0.0501	0.0202	0.1776	-0.0031	-0.0047	0.203	-0.0077	0.146	14.327	5.784	49.236
24	0.9832	-0.2962	0.0618	0.241	0.088	0.7969	-0.0471	-0.3191	-0.1117	0.0737	-0.0056	-0.0145	0.1566	0.0104	0.0526	0.1901	0.0108	0.0201	0.3136	0.0513	0.1002	2.914	-7.055	66.615

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 31
2	X-RAY DIFFRACTION	2	A	32 - 132
3	X-RAY DIFFRACTION	3	A	133 - 271
4	X-RAY DIFFRACTION	4	A	272 - 293
5	X-RAY DIFFRACTION	5	A	294 - 429
6	X-RAY DIFFRACTION	6	A	430 - 445
7	X-RAY DIFFRACTION	7	B	1 - 24
8	X-RAY DIFFRACTION	8	B	25 - 129
9	X-RAY DIFFRACTION	9	B	130 - 271
10	X-RAY DIFFRACTION	10	B	272 - 285
11	X-RAY DIFFRACTION	11	B	286 - 429
12	X-RAY DIFFRACTION	12	B	430 - 445
13	X-RAY DIFFRACTION	13	C	1 - 53
14	X-RAY DIFFRACTION	14	C	54 - 99
15	X-RAY DIFFRACTION	15	C	100 - 270
16	X-RAY DIFFRACTION	16	C	271 - 285
17	X-RAY DIFFRACTION	17	C	286 - 355
18	X-RAY DIFFRACTION	18	C	356 - 444
19	X-RAY DIFFRACTION	19	D	1 - 50
20	X-RAY DIFFRACTION	20	D	51 - 98
21	X-RAY DIFFRACTION	21	D	99 - 271
22	X-RAY DIFFRACTION	22	D	272 - 286
23	X-RAY DIFFRACTION	23	D	287 - 393
24	X-RAY DIFFRACTION	24	D	394 - 444

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