PDB-9eb8: Crystal Structure of Biotin Carboxylase from Ankistrodesmus in Co...

ID or keywords:

Entry

Database: PDB / ID: 9eb8

Title

Crystal Structure of Biotin Carboxylase from Ankistrodesmus in Complex with ADP

Components

Biotin carboxylase

Keywords

LIGASE / Biotin Carbixylase / enzyme

Function / homology

Function and homology information

biotin carboxylase / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / chloroplast / fatty acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function

Biological species

Ankistrodesmus falcatus (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Leonardo, D.A.C. / Vargas, J.A.S. / Mavila, A.M. / Furtado, A.A. / Pereira, H.M. / Garratt, R.C. / Castro, J.C.

Funding support

Peru, 2items

Organization	Grant number	Country
Programa Nacional de Innovacion Agraria (PNIA)	188-2018-INIA-PNIA-PASANTIA	Peru
Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica (CONCYTEC)	069-2019-FONDECYT	Peru

Citation

Journal: To Be Published
Title: Crystal Structure of Biotin Carboxylase from Ankistrodesmus
Authors: Leonardo, D.A.C. / Vargas, J.A.S. / Mavila, A.M. / Furtado, A.A. / Pereira, H.M. / Garratt, R.C. / Castro, J.C.

History

Deposition	Nov 12, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9eb8.cif.gz	563.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9eb8_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	9eb8_full_validation.pdf.gz	1.4 MB	Display
Data in XML	9eb8_validation.xml.gz	71.1 KB	Display
Data in CIF	9eb8_validation.cif.gz	98.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eb/9eb8 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/9eb8	HTTPS FTP

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Related structure data

Related structure data	9eb7C C: citing same article (ref.)
Similar structure data	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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (7) #192 - Dec 2015 Vancomycin similarity (4) #154 - Oct 2012 Citric Acid Cycle similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (4) #137 - May 2011 Cytochrome bc1 similarity (1)

Deposited unit

A: Biotin carboxylase

B: Biotin carboxylase

C: Biotin carboxylase

hetero molecules

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

1

A: Biotin carboxylase

hetero molecules

A: Biotin carboxylase

hetero molecules

defined by author
Evidence: gel filtration, light scattering
118 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Biotin carboxylase

C: Biotin carboxylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	177.777, 95.362, 95.194
Angle α, β, γ (deg.)	90.00, 92.67, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-868- HOH
2	1	A-892- HOH
3	1	A-905- HOH

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Protein , 1 types, 3 molecules ABC

#1: Protein	Biotin carboxylase / Acetyl-coenzyme A carboxylase biotin carboxylase subunit A Mass: 58371.453 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ankistrodesmus falcatus (plant) / Gene: accC / Plasmid: pET Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A2U8JGP4, biotin carboxylase

#1: Protein

Biotin carboxylase / Acetyl-coenzyme A carboxylase biotin carboxylase subunit A

Mass: 58371.453 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Ankistrodesmus falcatus (plant) / Gene: accC / Plasmid: pET Duet / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A2U8JGP4, biotin carboxylase

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Non-polymers , 5 types, 1124 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1107 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, 25% w/v PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97714 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 15, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97714 Å / Relative weight: 1
Reflection	Resolution: 1.9→47.68 Å / Num. obs: 124358 / % possible obs: 99.6 % / Redundancy: 5 % / CC_1/2: 0.913 / R_merge(I) obs: 0.302 / R_pim(I) all: 0.147 / R_rim(I) all: 0.337 / Χ²: 0.97 / Net I/σ(I): 5.4 / Num. measured all: 620270
Reflection shell	Resolution: 1.9→1.93 Å / % possible obs: 99.9 % / Redundancy: 4.6 % / R_merge(I) obs: 1.359 / Num. measured all: 28468 / Num. unique obs: 6126 / CC_1/2: 0.443 / R_pim(I) all: 0.69 / R_rim(I) all: 1.53 / Χ²: 1.02 / Net I/σ(I) obs: 1.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→47.68 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2167	6326	5.09 %	Radom selection
R_work	0.1777	-	-	-
obs	0.1797	124187	99.42 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→47.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10640	0	147	1107	11894

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10993
X-RAY DIFFRACTION	f_angle_d	0.88	14942
X-RAY DIFFRACTION	f_dihedral_angle_d	13.767	4044
X-RAY DIFFRACTION	f_chiral_restr	0.056	1659
X-RAY DIFFRACTION	f_plane_restr	0.007	1974

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 (%)
1.9-1.92	0.3083	201	0.2541	3917	X-RAY DIFFRACTION	100
1.92-1.94	0.2574	201	0.2359	3972	X-RAY DIFFRACTION	100
1.94-1.97	0.2594	198	0.2379	3881	X-RAY DIFFRACTION	100
1.97-1.99	0.2825	224	0.2298	3960	X-RAY DIFFRACTION	100
1.99-2.02	0.3037	225	0.2272	3921	X-RAY DIFFRACTION	100
2.02-2.05	0.2626	203	0.2199	3876	X-RAY DIFFRACTION	100
2.05-2.08	0.2721	187	0.213	3985	X-RAY DIFFRACTION	100
2.08-2.11	0.2481	221	0.2024	3933	X-RAY DIFFRACTION	100
2.11-2.14	0.222	198	0.1941	3891	X-RAY DIFFRACTION	100
2.14-2.17	0.2417	229	0.1962	3959	X-RAY DIFFRACTION	100
2.17-2.21	0.2427	219	0.1906	3892	X-RAY DIFFRACTION	100
2.21-2.25	0.2418	218	0.1856	3921	X-RAY DIFFRACTION	100
2.25-2.3	0.229	212	0.1781	3917	X-RAY DIFFRACTION	100
2.3-2.34	0.237	195	0.1817	3952	X-RAY DIFFRACTION	100
2.34-2.39	0.2281	213	0.1799	3954	X-RAY DIFFRACTION	100
2.39-2.45	0.245	195	0.1804	3962	X-RAY DIFFRACTION	100
2.45-2.51	0.233	213	0.1778	3920	X-RAY DIFFRACTION	100
2.51-2.58	0.2275	187	0.1812	3958	X-RAY DIFFRACTION	100
2.58-2.65	0.214	205	0.1824	3926	X-RAY DIFFRACTION	100
2.65-2.74	0.2312	196	0.1764	3950	X-RAY DIFFRACTION	100
2.74-2.84	0.2009	196	0.1782	3916	X-RAY DIFFRACTION	100
2.84-2.95	0.2154	220	0.1812	3971	X-RAY DIFFRACTION	100
2.95-3.09	0.2093	230	0.1875	3898	X-RAY DIFFRACTION	99
3.09-3.25	0.2314	241	0.1895	3893	X-RAY DIFFRACTION	99
3.25-3.45	0.1979	231	0.1788	3870	X-RAY DIFFRACTION	99
3.45-3.72	0.2084	216	0.1638	3878	X-RAY DIFFRACTION	98
3.72-4.09	0.2044	177	0.1549	3925	X-RAY DIFFRACTION	98
4.09-4.68	0.1767	221	0.1354	3881	X-RAY DIFFRACTION	98
4.68-5.9	0.1931	240	0.1611	3953	X-RAY DIFFRACTION	99
5.9-47.68	0.1696	214	0.1599	4029	X-RAY DIFFRACTION	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	1.6753	0.5413	0.0597	2.0085	-0.041	1.6673	0.0402	0.3193	0.0347	-0.2585	-0.0735	0.2014	0.0082	-0.156	0.0166	0.1939	0.0522	-0.0473	0.2379	-0.0139	0.1231	-6.2805	-7.8936	23.6457
2	1.4406	-0.4257	-0.2424	0.639	0.1799	0.6807	0.1478	0.2273	0.2598	-0.1837	-0.0507	-0.1354	-0.1766	-0.0216	-0.0898	0.2343	0.0267	0.0692	0.1951	0.0726	0.2278	17.2593	7.4559	22.7295
3	1.0124	0.1842	-0.2611	1.1973	0.0181	0.6036	0.044	-0.0106	0.0383	0.031	-0.0511	-0.1245	-0.0694	0.0045	0.0265	0.1251	0.0056	0.0039	0.1323	0.0066	0.128	8.7299	-4.1326	41.9626
4	2.6804	-0.2184	0.3747	0.7668	-0.1127	0.808	0.0276	-0.1024	-0.2357	0.1023	0.0256	0.0577	0.0553	-0.049	-0.0528	0.1484	0.0144	0.0137	0.1095	0.0084	0.1281	23.2551	-40.0089	39.7146
5	2.1586	-0.2011	-1.4607	2.7994	-0.8919	1.466	0.2281	-0.0933	0.4162	0.3638	-0.2093	0.1246	-0.4916	0.015	-0.0003	0.3571	-0.0524	-0.0635	0.2518	-0.064	0.3607	41.0126	-17.1353	47.9333
6	0.5925	-0.1661	0.0448	0.539	-0.2035	1.0683	0.0399	-0.0083	0.0106	-0.0207	-0.0285	-0.0765	-0.0326	0.0828	-0.0057	0.1537	0.0039	0.004	0.142	-0.0241	0.2015	35.2768	-32.0328	25.2064
7	0.8757	-0.18	-0.2507	1.918	0.1807	0.7153	-0.0179	0.1253	0.035	-0.2668	0.0536	-0.0229	-0.1868	-0.0451	-0.0302	0.1947	0.0061	-0.0039	0.1756	0.0034	0.0949	27.7933	-40.821	-13.0952
8	1.6326	0.3028	0.1744	1.0186	0.6387	1.7349	-0.0022	0.0125	-0.1439	-0.0075	-0.0025	0.0264	0.147	-0.1799	-0.0078	0.1457	-0.0042	0.0171	0.1225	-0.0218	0.1679	24.2596	-62.8295	-9.2628
9	1.2835	0.1358	-0.4565	0.9714	0.2147	0.736	0.0216	-0.1808	-0.0415	-0.0048	-0.0164	0.0041	-0.0049	-0.0461	-0.0048	0.1427	0.0093	-0.0283	0.2111	-0.0068	0.1264	20.075	-48.5304	6.9309

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 98 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 99 through 289 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 290 through 466 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 140 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 141 through 192 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 193 through 466 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid -1 through 140 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 141 through 289 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 290 through 464 )

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