PDB-4a10: Apo-structure of 2-octenoyl-CoA carboxylase reductase CinF from s...

ID or keywords:

Entry

Database: PDB / ID: 4a10

Title

Apo-structure of 2-octenoyl-CoA carboxylase reductase CinF from streptomyces sp.

Components

OCTENOYL-COA REDUCTASE/CARBOXYLASE

Keywords

OXIDOREDUCTASE / CCR / PKS BUILDING BLOCKS / ROSSMANN FOLD

Function / homology

Function and homology information

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

Biological species

STREPTOMYCES SP. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

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

Citation

Journal: Nat.Chem.Biol. / Year: 2011
Title: Unusual Carbon Fixation Giving Rise to Diverse Polyketide Extender Units
Authors: Quade, N. / Huo, L. / Rachid, S. / Heinz, D.W. / Muller, R.

History

Deposition	Sep 13, 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	Sep 27, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4a10.cif.gz	640.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4a10.ent.gz	529.6 KB	Display	PDB format
PDBx/mmJSON format	4a10.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4a10_validation.pdf.gz	454.8 KB	Display	wwPDB validaton report
Full document	4a10_full_validation.pdf.gz	468.8 KB	Display
Data in XML	4a10_validation.xml.gz	73 KB	Display
Data in CIF	4a10_validation.cif.gz	109.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a1/4a10 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/4a10	HTTPS FTP

-
Related structure data

Related structure data	4a0sC 3krtS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6na5-d 6na6-d 6na3-d 6na4-d 3krt-d 4a0s-d 6owe-d 3hzz-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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

192 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)	101.640, 85.220, 113.970
Angle α, β, γ (deg.)	90.00, 107.45, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	OCTENOYL-COA REDUCTASE/CARBOXYLASE / CINF 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1515 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

OCTENOYL-COA REDUCTASE/CARBOXYLASE / CINF

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: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1515 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48 % / Description: NONE
Crystal grow	pH: 7 / Details: 0.1M TRIS PH7, 20% GLYCEROL, 12% PEG8000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2010 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.1→48.48 Å / Num. obs: 107076 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / R_merge(I) obs: 0.16 / Net I/σ(I): 8.78
Reflection shell	Resolution: 2.1→2.25 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 3.7 / % possible all: 98.3

-
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: 2.25→48.48 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.862 / SU B: 15.311 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26867	4361	5 %	RANDOM
R_work	0.20943	-	-	-
obs	0.2124	82859	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: 19.906 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.59 Å²	0 Å²	-0.7 Å²
2-	-	0.25 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→48.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12537	0	0	1515	14052

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	12787
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.333	1.954	17377
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.994	5	1674
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.855	23.352	525
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.858	15	2001
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.313	15	103
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	1983
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	9723
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	0.367	1.5	8338
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.733	2	13286
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.438	3	4449
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.526	4.5	4090
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: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	317	-
R_work	0.254	6038	-
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	0.7791	-0.1234	-0.0823	1.1309	0.0331	0.9488	0.0156	-0.0871	-0.0697	0.1481	0.0424	-0.038	0.1368	-0.0002	-0.058	0.1614	-0.0235	0.0187	0.1261	0.0186	0.1387	-3.975	-21.993	43.895
2	0.658	0.143	-0.0924	0.1835	-0.1903	0.4136	0.0317	0.0126	-0.0216	-0.0258	-0.0035	0.0069	0.0782	0.0131	-0.0281	0.1559	-0.003	0.0254	0.1245	-0.0136	0.1452	4.287	-15.407	28.496
3	2.1347	-0.198	0.305	1.2782	0.2994	3.5245	0.0393	-0.0494	-0.2248	0.056	0.0155	-0.1236	0.4884	0.3206	-0.0547	0.1261	0.073	0.0196	0.0945	-0.0114	0.1646	27.068	-24.711	22.491
4	1.5584	0.3699	0.3039	1.1647	0.0382	1.1088	-0.0525	0.1034	-0.1257	0.0323	0.03	-0.1871	0.0768	0.2001	0.0225	0.1851	0.0084	0.039	0.1701	-0.0229	0.2083	16.832	-12.531	26.013
5	0.9668	-0.1852	-0.043	1.4531	-0.6389	1.6493	-0.0085	0.1409	-0.1531	-0.1013	0.0245	-0.0028	0.2548	0.0359	-0.0161	0.2047	-0.0444	0.0164	0.1132	-0.0354	0.189	-2.53	-29.332	23.925
6	0.9632	0.1923	0.2141	1.3853	-0.2373	0.8661	-0.0732	0.0151	0.1277	-0.05	0.0078	0.1576	-0.0535	-0.0716	0.0655	0.1264	0.03	0.0168	0.1302	-0.0284	0.1796	-6.18	20.365	40.622
7	1.1103	-1.3436	-0.2853	2.6521	1.0412	0.5543	0.0305	0.0561	-0.1352	-0.1563	-0.0977	0.1618	-0.0685	-0.0408	0.0672	0.1209	-0.0087	0.033	0.1156	-0.0222	0.1692	-0.252	10.123	33.005
8	0.8774	-0.039	-0.44	0.2001	0.0202	0.7399	-0.0099	0.0433	0.1208	0.0022	-0.0032	-0.0514	-0.1256	0.0534	0.0131	0.1308	-0.0153	0.0104	0.1104	0.0138	0.1836	17.167	19.846	36.491
9	1.7199	0.3613	0.035	2.132	0.2355	1.7073	-0.0562	0.3135	0.3215	-0.197	0.0279	0.038	-0.3109	-0.0178	0.0283	0.1267	-0.0186	0.0095	0.1095	0.0772	0.1711	25.085	25.313	19.85
10	0.7061	-0.1592	0.0666	0.7996	0.0798	0.5348	-0.0412	0.0009	0.1418	-0.0187	0.036	-0.0645	-0.0689	0.068	0.0052	0.1392	-0.0179	0.0088	0.1221	-0.0053	0.1953	14.01	23.271	38.914
11	1.7758	-1.4911	0.5167	2.6854	-0.3014	1.0929	0.0764	0.3117	0.0715	-0.1873	-0.162	-0.1312	0.0595	0.4168	0.0856	0.067	0.0363	0.0435	0.3283	0.1018	0.0601	38.839	5.654	-16.482
12	1.0859	-0.4131	0.7599	0.8674	-0.1338	1.2103	-0.0572	0.2083	0.1875	0.0353	-0.109	-0.0217	-0.1049	0.2612	0.1663	0.0549	0.008	0.036	0.2478	0.089	0.0942	39.322	7.099	-5.128
13	0.7126	0.0895	0.0082	0.5581	-0.0789	0.6638	0.0283	0.1518	0.0337	-0.0701	-0.0798	0.0019	0.0263	0.0843	0.0515	0.1181	0.0493	0.0249	0.207	0.0231	0.1281	25.634	-1.225	1.475
14	1.4338	-0.0252	0.4957	2.2259	0.6398	2.0067	-0.0064	0.0812	0.2196	-0.229	-0.0638	0.3	-0.234	-0.1997	0.0701	0.0745	0.0285	0.003	0.1489	0.0083	0.1514	4.332	7.642	7.93
15	0.4855	0.0354	0.2153	0.6359	-0.0002	0.6199	0.0161	0.1801	-0.0261	-0.1203	-0.0646	0.0681	0.1364	0.0771	0.0485	0.1279	0.0458	0.0208	0.2202	-0.0137	0.1052	23.024	-5.564	-7.535
16	1.6147	0.4504	-1.2942	5.5419	-2.1726	3.0347	0.1267	-0.0675	0.3008	-0.1407	-0.2896	-0.27	-0.2136	0.8411	0.1628	0.0398	-0.0798	-0.0086	0.3675	0.14	0.164	68.396	7.096	19.566
17	0.5834	-0.3361	0.5201	0.8252	-0.4021	1.3625	0.0724	0.0976	-0.0234	0.0031	-0.0369	-0.0167	0.2569	0.121	-0.0355	0.1034	0.0284	0.0191	0.1962	0.0379	0.1314	57.949	-11.382	26.118
18	0.9037	-0.2955	-0.1153	0.402	0.0201	0.5342	0.0001	0.054	0.0609	0.0534	-0.0567	-0.0596	0.0221	0.0713	0.0567	0.1094	-0.0087	0.0149	0.1586	0.0359	0.1474	44.471	1.771	29.185
19	1.0088	0.0981	-0.3125	0.9677	0.2332	0.8114	-0.0383	-0.1631	-0.1535	0.2522	-0.0482	-0.0413	0.1505	-0.0554	0.0864	0.1493	0.002	0.0165	0.1491	0.0387	0.1395	31.514	-3.988	41.657
20	1.2031	-0.1205	0.1185	1.3226	0.3999	0.5297	0.0134	-0.0599	0.2448	0.1378	-0.1068	-0.0933	-0.0415	0.0989	0.0934	0.1121	-0.006	-0.0132	0.1839	0.0196	0.1613	55.621	6.23	40.083

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 117
2	X-RAY DIFFRACTION	2	A	118 - 264
3	X-RAY DIFFRACTION	3	A	265 - 335
4	X-RAY DIFFRACTION	4	A	347 - 380
5	X-RAY DIFFRACTION	5	A	381 - 445
6	X-RAY DIFFRACTION	6	B	1 - 139
7	X-RAY DIFFRACTION	7	B	140 - 174
8	X-RAY DIFFRACTION	8	B	175 - 263
9	X-RAY DIFFRACTION	9	B	264 - 337
10	X-RAY DIFFRACTION	10	B	346 - 444
11	X-RAY DIFFRACTION	11	C	1 - 58
12	X-RAY DIFFRACTION	12	C	59 - 130
13	X-RAY DIFFRACTION	13	C	131 - 263
14	X-RAY DIFFRACTION	14	C	264 - 355
15	X-RAY DIFFRACTION	15	C	356 - 444
16	X-RAY DIFFRACTION	16	D	1 - 28
17	X-RAY DIFFRACTION	17	D	29 - 121
18	X-RAY DIFFRACTION	18	D	122 - 263
19	X-RAY DIFFRACTION	19	D	264 - 380
20	X-RAY DIFFRACTION	20	D	381 - 444

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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