PDB-4hr7: Crystal Structure of Biotin Carboxyl Carrier Protein-Biotin Carbo...

ID or keywords:

Entry

Database: PDB / ID: 4hr7

Title

Crystal Structure of Biotin Carboxyl Carrier Protein-Biotin Carboxylase Complex from E.coli

Components

Biotin carboxyl carrier protein of acetyl-CoA carboxylase
Biotin carboxylase

Keywords

LIGASE/BIOTIN BINDING PROTEIN / biotin carboxylase / biotin carboxyl carrier protein / acetyl-CoA carboxylase / protein-protein interaction / protein complex / protein interface / antibiotic target / ATP grasp / biotin-dependent carboxylase / fatty acid synthesis / LIGASE-BIOTIN BINDING PROTEIN complex

Function / homology

Function and homology information

biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / molecular adaptor activity / protein homodimerization activity / ATP binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.495 Å

Authors

Broussard, T.C. / Kobe, M.J. / Pakhomova, S. / Neau, D.B. / Price, A.E. / Champion, T.S. / Waldrop, G.L.

Citation

Journal: Structure / Year: 2013
Title: The three-dimensional structure of the biotin carboxylase-biotin carboxyl carrier protein complex of E. coli acetyl-CoA carboxylase.
Authors: Broussard, T.C. / Kobe, M.J. / Pakhomova, S. / Neau, D.B. / Price, A.E. / Champion, T.S. / Waldrop, G.L.

History

Deposition	Oct 26, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2013	Group: Database references
Revision 1.2	May 29, 2013	Group: Database references
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	4hr7.cif.gz	408 KB	Display	PDBx/mmCIF format
PDB format	pdb4hr7.ent.gz	330.5 KB	Display	PDB format
PDBx/mmJSON format	4hr7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4hr7_validation.pdf.gz	522.3 KB	Display	wwPDB validaton report
Full document	4hr7_full_validation.pdf.gz	539.1 KB	Display
Data in XML	4hr7_validation.xml.gz	72.1 KB	Display
Data in CIF	4hr7_validation.cif.gz	99.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hr/4hr7 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/4hr7	HTTPS FTP

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Related structure data

Related structure data	1bdoS 1dv1S S: Starting model for refinement
Similar structure data	4jad-1 4eiw-d 2dhr-d 0268 1owc-1 5ws5-2 21314 5z1a-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	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (4) #154 - Oct 2012 Citric Acid Cycle similarity (7) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (7) #192 - Dec 2015 Vancomycin similarity (4) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (4) #137 - May 2011 Cytochrome bc1 similarity (1)

Deposited unit

A: Biotin carboxylase

B: Biotin carboxyl carrier protein of acetyl-CoA carboxylase

C: Biotin carboxylase

D: Biotin carboxyl carrier protein of acetyl-CoA carboxylase

E: Biotin carboxylase

F: Biotin carboxylase

G: Biotin carboxyl carrier protein of acetyl-CoA carboxylase

I: Biotin carboxyl carrier protein of acetyl-CoA carboxylase

hetero molecules

274 kDa, 8 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)	232.995, 96.385, 120.573
Angle α, β, γ (deg.)	90.00, 120.15, 90.00
Int Tables number	5
Space group name H-M	C121

Details

QUATERNARY STRUCTURE IS AN (ALPHA)4(BETA)4 HETEROOCTAMER.

#1: Protein	Biotin carboxylase / Acetyl-CoA carboxylase subunit A / ACC Mass: 49386.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: accC, fabG, b3256, JW3224 / Plasmid: pAEP7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P24182, biotin carboxylase, acetyl-CoA carboxylase
#2: Protein	Biotin carboxyl carrier protein of acetyl-CoA carboxylase / BCCP Mass: 18872.521 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: accB, fabE, b3255, JW3223 / Plasmid: pAEP7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ABD8
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.14 Å³/Da / Density % sol: 42.63 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2012 / Details: KB mirrors
Radiation	Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.49→104.3 Å / Num. obs: 79251 / % possible obs: 98.6 % / Redundancy: 2.5 % / R_sym value: 0.062 / Net I/σ(I): 11.2
Reflection shell	Resolution: 2.49→2.63 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 11167 / R_sym value: 0.331 / % possible all: 95.4

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1DV1 AND 1BDO

1dv1

1bdo

Resolution: 2.495→104.26 Å / SU ML: 0.31 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Phase error: 24.79 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2291	3972	5.02 %	RANDOM
R_work	0.195	-	-	-
all	0.1968	79181	-	-
obs	0.1968	79181	98.37 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 38.07 Å²

Refinement step

Cycle: LAST / Resolution: 2.495→104.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15618	0	64	455	16137

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	15973
X-RAY DIFFRACTION	f_angle_d	0.718	21588
X-RAY DIFFRACTION	f_dihedral_angle_d	13.51	6016
X-RAY DIFFRACTION	f_chiral_restr	0.041	2416
X-RAY DIFFRACTION	f_plane_restr	0.003	2826

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 (%)
2.495-2.5254	0.3031	124	0.264	2313	X-RAY DIFFRACTION	85
2.5254-2.5573	0.3192	136	0.2707	2682	X-RAY DIFFRACTION	99
2.5573-2.591	0.3043	133	0.2496	2655	X-RAY DIFFRACTION	99
2.591-2.6265	0.2871	146	0.2452	2706	X-RAY DIFFRACTION	99
2.6265-2.664	0.2826	137	0.2461	2665	X-RAY DIFFRACTION	99
2.664-2.7038	0.2791	159	0.2369	2684	X-RAY DIFFRACTION	99
2.7038-2.746	0.2802	139	0.2317	2689	X-RAY DIFFRACTION	99
2.746-2.7911	0.2852	139	0.2373	2661	X-RAY DIFFRACTION	99
2.7911-2.8392	0.3036	150	0.2269	2679	X-RAY DIFFRACTION	99
2.8392-2.8908	0.2971	140	0.2257	2684	X-RAY DIFFRACTION	99
2.8908-2.9464	0.2467	134	0.235	2703	X-RAY DIFFRACTION	99
2.9464-3.0066	0.2458	130	0.2243	2705	X-RAY DIFFRACTION	99
3.0066-3.072	0.2584	151	0.2165	2685	X-RAY DIFFRACTION	99
3.072-3.1434	0.2302	137	0.2169	2719	X-RAY DIFFRACTION	99
3.1434-3.222	0.2398	133	0.2232	2696	X-RAY DIFFRACTION	99
3.222-3.3092	0.2628	147	0.2175	2685	X-RAY DIFFRACTION	99
3.3092-3.4065	0.25	128	0.2148	2725	X-RAY DIFFRACTION	99
3.4065-3.5165	0.2239	140	0.2077	2701	X-RAY DIFFRACTION	99
3.5165-3.6422	0.2193	143	0.1957	2709	X-RAY DIFFRACTION	99
3.6422-3.788	0.2375	137	0.1927	2679	X-RAY DIFFRACTION	99
3.788-3.9604	0.236	152	0.1753	2715	X-RAY DIFFRACTION	99
3.9604-4.1692	0.233	139	0.1643	2717	X-RAY DIFFRACTION	99
4.1692-4.4305	0.1859	153	0.1491	2693	X-RAY DIFFRACTION	99
4.4305-4.7725	0.1732	147	0.1509	2726	X-RAY DIFFRACTION	99
4.7725-5.2528	0.174	150	0.1573	2730	X-RAY DIFFRACTION	99
5.2528-6.0128	0.2007	154	0.1796	2729	X-RAY DIFFRACTION	99
6.0128-7.5752	0.2042	138	0.1948	2750	X-RAY DIFFRACTION	99
7.5752-104.3511	0.1956	156	0.1655	2724	X-RAY DIFFRACTION	96

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	0.0894	0.0259	0.0828	0.0699	0.0337	0.0696	0.028	0.2226	0.1415	-0.1027	0.1708	0.1287	-0.2207	-0.129	0.6652	0.2335	0.0388	0.1025	0.1716	0.1866	-0.0611	193.9519	53.1575	21.0037
2	0.0661	0.0642	0.0234	0.0862	0.0299	0.0687	-0.0429	-0.0361	-0.023	0.0922	0.0534	-0.049	-0.1307	-0.0284	0.1134	0.2782	0.0789	0.0533	0.281	0.1254	0.1759	178.1703	50.4623	35.9411
3	0.1792	0.0716	0.0382	0.139	0.1294	0.1802	0.0883	0.0028	-0.0943	0.0882	0.1203	0.1182	-0.0399	-0.1046	0.5451	0.225	0.0341	0.0565	0.2286	0.1188	0.1468	190.3989	36.7733	25.9636
4	0.0392	0.0309	-0.013	0.0738	-0.0019	0.005	0.0467	0.0743	0.0256	-0.0073	0.0743	-0.0366	-0.0135	-0.0549	0.0632	0.3316	0.0061	0.0583	0.263	-0.0398	0.0647	213.1941	57.4118	41.7092
5	0.0096	0.0036	-0.0127	0.2678	-0.0373	0.026	0.0274	0.0296	0.042	0.116	0.0127	-0.0445	-0.1097	-0.0027	-0.003	0.2549	0.0483	0.0753	0.1774	-0.0149	0.1333	211.2585	61.4737	42.7055
6	0.0712	-0.0243	-0.0624	0.135	-0.0489	0.0904	0.0665	0.0878	-0.4285	0.0853	0.0618	-0.0166	0.1682	-0.0446	0.0147	0.2706	-0.02	-0.0428	0.2195	-0.0035	0.4684	195.8741	-0.0047	21.0725
7	0.0077	-0.0037	-0.0089	0.0025	0.0007	0.0076	0.0038	0.008	-0.1073	-0.0227	0.0005	-0.0307	-0.0114	0.0532	0	0.3526	-0.0579	0.0402	0.4991	-0.2269	0.4966	193.6887	-7.5695	-18.8412
8	0.047	-0.075	0.0064	0.3104	-0.031	0.154	-0.0441	0.2783	-0.2008	0.0164	0.1444	0.0103	0.0386	0.0073	0.177	0.141	-0.0546	-0.0064	0.2563	-0.0509	0.2251	195.4273	14.2392	5.9119
9	0.004	-0.0021	0.0044	0.0045	0.0035	0.0105	0.0204	0.0876	0.0273	-0.0394	-0.0139	-0.0376	0.0413	-0.0346	-0	0.4801	0.0317	0.0122	0.4309	-0.261	0.7064	220.2505	-12.6164	3.9407
10	0.0041	-0.0055	-0.0074	0.0066	0.0059	0.0123	0.0188	-0.008	0.0511	-0.0952	-0.002	-0.0586	0.1198	0.001	-0	0.4802	0.0149	-0.0203	0.3971	-0.2164	0.6967	221.1547	-10.0542	8.188
11	0.0485	0.0082	0.0149	0.2287	-0.1275	0.1095	-0.0566	-0.0413	0.0776	-0.0233	0.094	0.0831	-0.1119	0.0091	0.0997	0.2058	-0.0295	0.0258	0.1667	-0.0585	0.0903	239.6807	49.24	36.6171
12	0.0164	0.011	0.013	0.0165	-0.0263	0.0304	0.0632	0.0634	0.0022	-0.0792	0.0202	-0.0114	-0.0728	0.0428	0.1536	0.3044	-0.0168	0.0953	0.4455	-0.0844	0.0936	262.3099	48.8129	17.1203
13	0.1883	-0.1156	0.0479	0.0705	-0.0427	0.028	0.1517	0.1462	-0.2224	0.0237	0.0079	-0.0038	0.0254	0.1527	0.2785	0.1826	0.0172	-0.0059	0.2806	-0.0952	0.1269	247.1735	33.9669	26.3688
14	0.1502	-0.0478	-0.0078	0.0268	0.0025	0.0211	0.0363	0.0182	-0.4212	-0.0709	0.0571	0.0466	0.1491	0.0739	0.1072	0.3241	0.064	-0.1977	0.1744	-0.0624	0.7949	237.6162	-2.309	28.1942
15	-0.0063	0.0037	0.0051	0.1411	0.1162	0.1162	0.0578	-0.1698	-0.2985	0.0117	0.0311	0.0505	0.0709	0.0066	0.1927	0.2221	0.0205	-0.0815	0.3621	0.1861	0.57	245.4905	0.5001	52.6273
16	0.1367	-0.0576	-0.2035	0.0904	0.1459	0.3901	0.0861	-0.2453	-0.1284	-0.0621	0.1074	0.0785	-0.0209	-0.065	0.1574	0.181	-0.0015	-0.061	0.2529	0.0761	0.3559	229.2288	17.0355	44.135
17	0.008	0.0001	-0.0016	0.0082	-0.0008	0.0068	0.0052	-0.0695	0.0608	0.0388	0.0114	-0.0327	0.0263	-0.0424	0	0.5269	-0.0117	-0.1334	0.3873	0.1485	0.6159	211.0651	-14.2015	42.8594
18	0.0037	0.0049	-0.0083	0.0045	-0.0097	0.0231	-0.1139	-0.0147	-0.0174	0.1277	-0.0515	-0.079	0.0945	0.0863	0	0.4529	-0.0542	-0.1102	0.3784	0.1973	0.7308	212.5412	-12.5008	39.1711
19	0.03	0.0339	-0.0261	0.0391	-0.0285	0.0187	-0.0162	0.07	0.0954	0.0109	-0.0088	-0.0254	-0.0267	0.1057	-0.0222	0.3076	-0.1572	0.0938	0.4192	0.0941	0.1516	228.7984	64.0571	11.0577
20	0.0075	0.0009	-0.0072	0.0115	-0.0075	0.0088	0.0209	0.0501	-0.012	-0.0395	-0.0259	-0.0308	-0.0347	0.1402	-0	0.2917	-0.0191	0.0818	0.311	0.019	0.2181	226.1755	59.7648	12.8542

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:167)
2	X-RAY DIFFRACTION	2	(chain A and resid 168:248)
3	X-RAY DIFFRACTION	3	(chain A and resid 249:446)
4	X-RAY DIFFRACTION	4	(chain B and resid 77:96)
5	X-RAY DIFFRACTION	5	(chain B and resid 97:156)
6	X-RAY DIFFRACTION	6	(chain C and resid 1:128)
7	X-RAY DIFFRACTION	7	(chain C and resid 129:203)
8	X-RAY DIFFRACTION	8	(chain C and resid 204:446)
9	X-RAY DIFFRACTION	9	(chain D and resid 80:113)
10	X-RAY DIFFRACTION	10	(chain D and resid 114:156)
11	X-RAY DIFFRACTION	11	(chain E and resid 1:138)
12	X-RAY DIFFRACTION	12	(chain E and resid 139:238)
13	X-RAY DIFFRACTION	13	(chain E and resid 239:446)
14	X-RAY DIFFRACTION	14	(chain F and resid 1:126)
15	X-RAY DIFFRACTION	15	(chain F and resid 127:338)
16	X-RAY DIFFRACTION	16	(chain F and resid 339:446)
17	X-RAY DIFFRACTION	17	(chain G and resid 80:108)
18	X-RAY DIFFRACTION	18	(chain G and resid 109:156)
19	X-RAY DIFFRACTION	19	(chain I and resid 80:118)
20	X-RAY DIFFRACTION	20	(chain I and resid 119:156)

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Yorodumi