PDB-4fb8: Crystal Structure of apo Acyl-CoA Carboxylase

ID or keywords:

Entry

Database: PDB / ID: 4fb8

Title

Crystal Structure of apo Acyl-CoA Carboxylase

Components

Probable propionyl-CoA carboxylase beta chain 6

Keywords

LIGASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Crotonase fold / Acyl-CoA Carboxylase / PSI-2 / Protein Structure Initiative

Function / homology

Function and homology information

acetyl-CoA carboxytransferase / Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / fatty acid elongation, saturated fatty acid / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / ligase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / transferase activity
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3 Å

Authors

Reddy, M.C.M. / Bruning, J.B. / Sherekar, M. / Valluru, S. / Ehrenfeld, H. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2014
Title: Structure, Activity, and Inhibition of the Carboxyltransferase beta-Subunit of Acetyl Coenzyme A Carboxylase (AccD6) from Mycobacterium tuberculosis.
Authors: Reddy, M.C. / Breda, A. / Bruning, J.B. / Sherekar, M. / Valluru, S. / Thurman, C. / Ehrenfeld, H. / Sacchettini, J.C.

History

Deposition	May 22, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Aug 13, 2014	Group: Database references
Revision 1.2	Oct 1, 2014	Group: Database references
Revision 1.3	Nov 15, 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
Revision 1.4	Sep 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4fb8.cif.gz	304.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4fb8.ent.gz	246 KB	Display	PDB format
PDBx/mmJSON format	4fb8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4fb8_validation.pdf.gz	448.9 KB	Display	wwPDB validaton report
Full document	4fb8_full_validation.pdf.gz	501.4 KB	Display
Data in XML	4fb8_validation.xml.gz	36.3 KB	Display
Data in CIF	4fb8_validation.cif.gz	48.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fb/4fb8 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/4fb8	HTTPS FTP

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Related structure data

Related structure data	4g2rC 1xnvS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4g2r-d 6pk2-1 6tzv-3 6prw-1 6prw-3 6tzv-1 6prw-4 4beb-2 3fwn-d 6p7u-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
Other databases	TargetTrack: TB-Rv2247

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Probable propionyl-CoA carboxylase beta chain 6

B: Probable propionyl-CoA carboxylase beta chain 6

100 kDa, 2 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)	82.284, 82.361, 157.870
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Probable propionyl-CoA carboxylase beta chain 6 / PCCase / Propanoyl-CoA:carbon dioxide ligase Mass: 50198.934 Da / Num. of mol.: 2 / Fragment: AccD6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: accD6, MT2307, MTCY427.28, Rv2247 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P63407, UniProt: P9WQH5*PLUS, propionyl-CoA carboxylase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Probable propionyl-CoA carboxylase beta chain 6 / PCCase / Propanoyl-CoA:carbon dioxide ligase

Mass: 50198.934 Da / Num. of mol.: 2 / Fragment: AccD6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: accD6, MT2307, MTCY427.28, Rv2247 / Plasmid: pET28 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63407, UniProt: P9WQH5*PLUS, propionyl-CoA carboxylase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.66 Å³/Da / Density % sol: 53.83 %
Crystal grow	Temperature: 289 K / pH: 7.5 Details: 60% tacsimate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91963
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 9, 2011 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91963 Å / Relative weight: 1
Reflection twin	Operator: K,H,-L / Fraction: 0.479
Reflection	Resolution: 3→50 Å / Num. obs: 21541 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 11.9 % / R_merge(I) obs: 0.152 / R_sym value: 0.152 / Net I/σ(I): 8
Reflection shell	Resolution: 3→3.05 Å / Redundancy: 8.7 % / R_merge(I) obs: 0.881 / % possible all: 90.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1XNV

1xnv

Resolution: 3→46.85 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / σ(F): 1.34 / Phase error: 29.92 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.304	1096	5.31 %
R_work	0.233	-	-
obs	0.236	20652	93.5 %
all	-	20652	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 57.12 Å² / k_sol: 0.33 e/Å³

Displacement parameters

B_iso mean: 49.77 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-10.0925 Å²	-0 Å²	-0 Å²
2-	-	-3.6899 Å²	-0 Å²
3-	-	-	-10.5296 Å²

Refinement step

Cycle: LAST / Resolution: 3→46.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6215	0	0	5	6220

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6334
X-RAY DIFFRACTION	f_angle_d	1.253	8614
X-RAY DIFFRACTION	f_dihedral_angle_d	19.175	2192
X-RAY DIFFRACTION	f_chiral_restr	0.078	998
X-RAY DIFFRACTION	f_plane_restr	0.006	1142

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 (%)
3.0148-3.1736	0.3929	101	0.2166	2037	X-RAY DIFFRACTION	66
3.1736-3.3723	0.3099	143	0.2114	2780	X-RAY DIFFRACTION	92
3.3723-3.6325	0.302	165	0.2178	2835	X-RAY DIFFRACTION	92
3.6325-3.9976	0.299	150	0.2115	2880	X-RAY DIFFRACTION	93
3.9976-4.575	0.2692	172	0.1974	2936	X-RAY DIFFRACTION	94
4.575-5.7602	0.2624	149	0.2453	2984	X-RAY DIFFRACTION	95
5.7602-35.8658	0.3635	161	0.2882	3105	X-RAY DIFFRACTION	95

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	0.0005	-0.0001	0.0002	0.0012	-0.0015	0.0008	0.0042	-0.0099	0.0017	-0.0054	0.0007	-0.0014	-0.0002	-0.0032	0.0062	0.0962	-0.0211	0.036	0.1267	0.0379	0.1187	22.663	-23.1766	3.6778
2	0.018	-0.0109	-0.0112	0.0129	-0.0021	0.019	0.0252	-0.0132	0.0075	0.0137	0.017	0.0203	-0.0185	-0.0154	0.0735	-0.045	0.0055	0.0808	-0.0198	0.0132	0.0586	29.8991	-15.076	-3.9607
3	0.0208	-0.0147	-0.0035	0.0144	0.0082	0.0115	0.0023	-0.0135	-0.0017	0.0011	0.0077	0.0013	0.0003	-0.0071	0.012	-0.0014	-0.0142	0.0553	0.025	0.0732	0.1563	13.9705	-14.8984	-9.7063
4	0.0022	-0.0006	0.0011	-0.0005	0	-0.0003	-0.014	0.0004	0.0002	-0.0116	0.0107	0.0124	0.0054	-0.004	-0.0008	0.094	-0.0483	0.0374	0.1127	0.0194	0.1611	11.1413	-35.8605	-30.3207
5	0.0058	0.0033	-0.0017	0.0014	0.0002	0.0026	0.0101	-0.0002	0.0069	-0.0043	0.0039	0.0168	0.0051	-0.0097	0.0119	-0.0033	-0.0155	-0.0317	0.0663	0.0113	0.084	5.6845	-21.0633	-30.2908
6	0.0095	0.0082	-0.0015	0.0083	-0.0052	0.0037	0.0049	0.0141	0.0078	-0.0031	0.0096	0.0254	0.0078	-0.0285	0.018	-0.0966	0.0344	-0.012	-0.0523	0.0389	0.1241	18.5588	-14.9141	-29.0345
7	0.0035	-0	0.0057	0.001	-0.0016	0.0084	0.0041	0.0119	0.0053	0.0035	-0.0007	-0.0059	-0.0025	-0.017	0.0021	0.0062	0.0177	-0.0347	0.0181	0.0156	0.0718	19.1734	-19.3799	-38.6837
8	0.0024	0.002	0.0018	0.0014	-0.003	0.0029	-0.0014	0.0165	0.0037	0.0044	-0.0074	0.0061	0.0059	-0.0195	-0.0159	0.0992	-0.0142	-0.0569	0.0472	0.0242	0.113	14.9036	-14.1957	-49.5841
9	-0	-0.0005	0.0007	0.0008	0.0016	0.0017	0.003	0.0029	0.0047	0.0023	0.0001	0.0048	-0.0047	0.0046	-0	0.583	-0.0105	-0.0321	0.5599	-0.0051	0.5376	6.3085	-10.3071	-56.3318
10	0.0169	-0.0037	0.0285	0.0004	-0.0024	0.05	0.01	0.0167	0.0116	-0.019	0.0271	0.0279	0.0133	-0.0304	0.0432	0.0347	-0.0567	0.0487	0.001	0.0283	0.0692	20.0684	-30.096	-37.4905
11	-0.0014	0.006	0.0009	0.0367	0.014	0.0113	0.0229	0.0336	-0.0116	-0.0501	0.0195	-0.01	-0.0333	-0.0044	0.0773	0.0518	-0.0316	0.0338	-0.2035	0.0134	0.0412	38.5799	-6.423	-47.1465
12	-0.003	-0.0038	0.0045	0.044	-0.0265	0.015	-0.0045	-0.015	0.0246	0.0198	-0.022	-0.0009	-0.0332	0.0191	-0.0576	0.0335	-0.0018	0.034	-0.1312	0.0171	0.1108	41.486	8.0801	-29.3749
13	0.0756	-0.0171	-0.0174	0.0315	0.0064	0.0141	-0.0259	0.0089	0.0115	-0.0057	-0.0031	-0.0214	-0.0016	-0.0062	-0.0661	0.0097	-0.0324	0.0397	-0.0518	0.0077	0.1152	38.7572	3.3027	-20.2992
14	0.0363	-0.0375	0.0075	0.0412	-0.0087	0.0575	0.0197	-0.0106	0.0193	0.0145	0.04	-0.0086	-0.0287	-0.0044	0.0859	-0.0263	0.0522	0.0155	-0.0324	-0.0434	0.1089	37.0706	0.8043	-9.5221
15	0.0007	0.001	-0.0012	0.0012	-0.0012	0.0017	0.0076	0.0078	0.0057	-0.0036	0.0105	0.0017	0.0055	0.0088	0	0.1395	-0.0155	0.0541	0.1306	-0.0254	0.136	25.1623	13.3366	12.3382
16	0.0029	-0.0005	-0.0048	-0.0006	0.0026	0.0105	0.02	-0.0089	0.0035	0.0014	0.0029	-0.0126	-0.0186	0.0109	0.0107	0.0477	-0.032	0.027	0.0774	-0	0.113	51.2499	1.3771	-6.2082

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 14:69)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 70:147)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 148:213)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 214:233)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 234:262)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 263:350)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 351:373)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 374:408)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 409:436)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 437:470)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 16:145)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 146:268)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 269:312)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 313:399)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 400:428)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 429:465)

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