PDB-4asi: Crystal structure of human ACACA C-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 4asi

Title

Crystal structure of human ACACA C-terminal domain

Components

ACETYL-COA CARBOXYLASE 1

Keywords

LIGASE / PROTEIN

Function / homology

Function and homology information

fatty-acyl-CoA biosynthetic process / Defective HLCS causes multiple carboxylase deficiency / acetyl-CoA carboxylase / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / ChREBP activates metabolic gene expression / acetyl-CoA carboxylase activity / tissue homeostasis ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Froese, D.S. / Muniz, J.R.C. / Kiyani, W. / Krojer, T. / Vollmar, M. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U. / Yue, W.W.

Citation

Journal: To be Published
Title: Crystal Structure of Human Acaca C-Terminal Domain
Authors: Froese, D.S. / Muniz, J.R.C. / Kiyani, W. / Krojer, T. / Vollmar, M. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U. / Yue, W.W.

History

Deposition	May 1, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2	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	4asi.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb4asi.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	4asi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4asi_validation.pdf.gz	471.3 KB	Display	wwPDB validaton report
Full document	4asi_full_validation.pdf.gz	515.1 KB	Display
Data in XML	4asi_validation.xml.gz	140.8 KB	Display
Data in CIF	4asi_validation.cif.gz	193.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/as/4asi ftp://data.pdbj.org/pub/pdb/validation_reports/as/4asi	HTTPS FTP

-
Related structure data

Related structure data	2x24S 3ff6S 2yl2 S: Starting model for refinement
Similar structure data	3ff6-1 3ff6-2 5cte-d 3tdc-2 1od2-d 4wyo-d 3pih-d 4jeh-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2x24S

3ff6S

2yl2

S: Starting model for refinement

Similar structure data

-
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) #155 - Nov 2012 Vitamin D Receptor similarity (1) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (4) #137 - May 2011 Cytochrome bc1 similarity (1)

Deposited unit

A: ACETYL-COA CARBOXYLASE 1

B: ACETYL-COA CARBOXYLASE 1

C: ACETYL-COA CARBOXYLASE 1

D: ACETYL-COA CARBOXYLASE 1

E: ACETYL-COA CARBOXYLASE 1

F: ACETYL-COA CARBOXYLASE 1

525 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ACETYL-COA CARBOXYLASE 1

C: ACETYL-COA CARBOXYLASE 1

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

2

B: ACETYL-COA CARBOXYLASE 1

D: ACETYL-COA CARBOXYLASE 1

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

3

E: ACETYL-COA CARBOXYLASE 1

F: ACETYL-COA CARBOXYLASE 1

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

Unit cell

Length a, b, c (Å)	109.966, 143.712, 540.072
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	ACETYL-COA CARBOXYLASE 1 / ACC1 / ACC-ALPHA / BIOTIN CARBOXYLASE / 6.3.4.14 Mass: 87500.992 Da / Num. of mol.: 6 / Fragment: C-TERMINAL DOMAIN, RESIDUES 1493-2260 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q13085, acetyl-CoA carboxylase, biotin carboxylase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

ACETYL-COA CARBOXYLASE 1 / ACC1 / ACC-ALPHA / BIOTIN CARBOXYLASE / 6.3.4.14

Mass: 87500.992 Da / Num. of mol.: 6 / Fragment: C-TERMINAL DOMAIN, RESIDUES 1493-2260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: Q13085, acetyl-CoA carboxylase, biotin carboxylase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 29 / 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: 4.07 Å³/Da / Density % sol: 69.83 % / Description: NONE
Crystal grow	Details: 0.05M NA MALONATE; 19% (W/V) PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
Detector	Type: ADSC CCD / Detector: CCD / Date: Oct 5, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.8→143.71 Å / Num. obs: 207126 / % possible obs: 98.4 % / Observed criterion σ(I): 0.8 / Redundancy: 4.1 % / B_iso Wilson estimate: 85.8 Å² / R_merge(I) obs: 0.17 / Net I/σ(I): 8
Reflection shell	Resolution: 2.8→2.95 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 0.8 / % possible all: 98.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2X24 AND 3FF6

2x24

3ff6

Resolution: 2.8→540.07 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.937 / SU B: 32.678 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.442 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23589	10400	5 %	RANDOM
R_work	0.20197	-	-	-
obs	0.20367	196369	97.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 85.265 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.82 Å²	0 Å²	0 Å²
2-	-	0.63 Å²	0 Å²
3-	-	-	-6.45 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→540.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34287	0	0	29	34316

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	35153
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	23564
X-RAY DIFFRACTION	r_angle_refined_deg	1.432	1.953	47844
X-RAY DIFFRACTION	r_angle_other_deg	1.227	3	57164
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.878	5	4429
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.405	23.371	1581
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.848	15	5563
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.177	15	270
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	5285
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	39635
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	7419
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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: 2.8→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.46	723	-
R_work	0.431	13619	-
obs	-	-	96.79 %

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	5.0927	1.2213	0.0051	1.4551	-0.0389	0.8144	0.0216	0.3776	0.0375	-0.1306	-0.0198	0.3603	-0.169	-0.1254	-0.0018	0.1203	0.0059	-0.0814	0.0987	-0.0298	0.1453	10.857	-13.1818	-140.5269
2	2.268	0.485	0.8926	1.0311	0.1086	2.5062	-0.1142	-0.2243	0.192	0.1721	-0.0051	0.1271	-0.2636	-0.2085	0.1192	0.1271	0.0349	-0.0253	0.0307	-0.0184	0.1511	27.4926	-5.1853	-114.6973
3	0.3625	0.0555	0.2522	1.1874	1.0246	1.7625	-0.0622	-0.0315	-0.2446	0.2726	0.0218	-0.0991	0.3022	0.2944	0.0404	0.3246	0.0141	-0.0528	0.2744	0.0182	0.4166	50.3959	-17.64	-103.3702
4	4.6746	-1.1992	-0.5121	1.2899	0.5113	1.3219	0.0865	-0.2752	0.1381	0.0284	0.0352	-0.2822	-0.1467	0.2065	-0.1217	0.1368	-0.1101	-0.0736	0.1872	0.0349	0.1091	46.8813	-14.1702	-161.9108
5	1.7185	-0.4959	0.8665	1.0852	0.0989	3.223	0.0228	0.2748	0.2242	-0.3104	-0.0868	-0.0698	-0.5142	-0.1264	0.064	0.4004	0.0172	-0.0384	0.2374	0.0721	0.1366	29.9324	-5.925	-189.1094
6	0.4365	-0.0042	0.1744	0.6371	0.3919	2.1538	-0.0585	0.0828	-0.1904	-0.096	-0.0746	0.2414	-0.0926	-0.7314	0.1331	0.4149	0.121	-0.1558	0.7417	0.018	0.4524	6.8178	-13.6279	-201.1351
7	1.7841	1.1989	0.9763	1.8774	1.1203	1.4151	0.2567	-0.5568	-0.3302	0.6395	-0.109	-0.0814	0.2042	-0.1629	-0.1477	0.5022	-0.0435	-0.0862	0.2793	0.1863	0.2589	31.5211	-27.0408	-89.6351
8	2.2218	-0.5681	1.5445	0.983	-0.6354	1.5002	0.0195	-0.3077	-0.0735	0.2456	-0.059	0.3286	0.0012	-0.3824	0.0395	0.0902	-0.0955	0.0875	0.2499	-0.0243	0.4343	-2.1081	-24.2308	-120.026
9	9.0271	0.082	-2.8977	0.0193	-0.078	1.232	0.1461	0.3103	-0.6531	-0.084	-0.0517	-0.0241	0.2757	0.0876	-0.0944	0.5389	0.1462	-0.1381	0.2249	-0.1188	0.808	31.0026	-50.88	-132.1202
10	1.5632	-1.4551	0.6959	2.9108	-1.2064	2.234	0.1588	0.5319	-0.1506	-0.5515	-0.1355	0.2689	-0.1039	-0.467	-0.0232	0.513	-0.0835	-0.1525	0.6235	-0.0628	0.1779	21.0308	-27.7189	-213.2247
11	1.7754	-0.0837	0.7634	1.992	-0.0552	2.534	0.0391	0.3164	0.0691	-0.2667	-0.0223	-0.1131	-0.1473	0.1814	-0.0168	0.2414	-0.0953	-0.0077	0.2519	-0.0003	0.109	47.8769	-29.5397	-195.2628
12	1.8911	0.1964	0.7873	1.2492	0.4328	1.0195	-0.0611	-0.1674	0.0935	0.1249	0.0567	0.3017	0.2855	-0.0801	0.0044	0.3355	-0.0414	0.0395	0.2864	0.0219	0.2505	50.9736	-34.328	-169.4697
13	0.9105	-0.4586	0.3139	1.899	-0.7259	3.3958	0.0644	-0.1159	0.0779	0.1048	0.0098	0.0362	-0.2203	-0.4713	-0.0742	0.6746	0.042	0.0477	0.6684	0.0141	0.1777	54.2196	-62.795	-241.7295
14	2.2207	-0.4672	-2.5122	0.2672	0.5128	3.7102	-0.205	-0.0452	-0.1623	-0.2416	0.0864	0.2009	-0.3296	-0.3057	0.1186	1.198	0.1797	0.0078	0.9361	0.1333	0.3713	57.2196	-52.5058	-285.2089
15	4.9457	0.8113	2.5833	3.6513	0.9336	1.4809	0.9698	-0.2575	1.569	-0.2886	-2.31	2.561	0.2495	-0.8198	1.3403	0.6834	0.4851	-0.0541	3.6195	-1.3002	2.1232	22.7126	-52.6925	-264.7563
16	0.9421	-0.2034	-0.0502	1.9871	-0.8818	3.2351	0.2066	0.358	-0.1596	-0.5979	-0.089	0.108	0.7772	-0.373	-0.1176	1.1104	-0.0998	-0.0564	0.7546	-0.0526	0.2219	55.9785	-81.328	-268.4938
17	3.6082	0.1692	4.9416	0.3039	0.5643	8.8835	-0.0691	0.1429	-0.2344	0.0549	0.2577	0.188	0.9148	-0.0686	-0.1886	1.1903	-0.1609	0.0132	0.5013	0.078	0.3243	63.3653	-91.9186	-221.7033
18	1.8065	-0.1495	0.0059	0.2978	-0.3749	0.7246	0.1306	0.1235	-0.4983	0.0271	0.1247	0.3842	0.2047	-0.8765	-0.2553	1.5038	-0.841	-0.1452	2.1468	0.013	1.4567	24.5564	-93.7179	-245.1311

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1618 - 1824
2	X-RAY DIFFRACTION	2	A	1825 - 2159
3	X-RAY DIFFRACTION	3	A	2160 - 2375
4	X-RAY DIFFRACTION	4	B	1618 - 1824
5	X-RAY DIFFRACTION	5	B	1825 - 2169
6	X-RAY DIFFRACTION	6	B	2170 - 2361
7	X-RAY DIFFRACTION	7	C	1618 - 1955
8	X-RAY DIFFRACTION	8	C	1956 - 2257
9	X-RAY DIFFRACTION	9	C	2258 - 2375
10	X-RAY DIFFRACTION	10	D	1618 - 1886
11	X-RAY DIFFRACTION	11	D	1887 - 2143
12	X-RAY DIFFRACTION	12	D	2144 - 2375
13	X-RAY DIFFRACTION	13	E	1620 - 2160
14	X-RAY DIFFRACTION	14	E	2161 - 2296
15	X-RAY DIFFRACTION	15	E	2297 - 2347
16	X-RAY DIFFRACTION	16	F	1620 - 2149
17	X-RAY DIFFRACTION	17	F	2150 - 2269
18	X-RAY DIFFRACTION	18	F	2270 - 2346

-
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