PDB-6hxn: Structure of the citryl-CoA lyase core module of Chlorobium limic...

ID or keywords:

Entry

Database: PDB / ID: 6hxn

Title

Structure of the citryl-CoA lyase core module of Chlorobium limicola ATP citrate lyase (space group P3121)

Components

ATP-citrate lyase alpha-subunit

Keywords

LYASE / ATP citrate lyase / central metabolism / acetyl-Coa / citrate shuttle / rTCA cycle / citryl-CoA / lipogenesis

Function / homology

Function and homology information

citrate synthase (unknown stereospecificity) / ATP citrate synthase activity / acetyl-CoA biosynthetic process / tricarboxylic acid cycle / fatty acid biosynthetic process / lyase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Chlorobium limicola (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Verstraete, K. / Verschueren, K.

Funding support

Belgium, 1items

Citation

Journal: Nature / Year: 2019
Title: Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.
Authors: Verschueren, K.H.G. / Blanchet, C. / Felix, J. / Dansercoer, A. / De Vos, D. / Bloch, Y. / Van Beeumen, J. / Svergun, D. / Gutsche, I. / Savvides, S.N. / Verstraete, K.

History

Deposition	Oct 17, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	May 8, 2019	Group: Data collection / Database references Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	May 1, 2024	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

-
Download

PDBx/mmCIF format	6hxn.cif.gz	223 KB	Display	PDBx/mmCIF format
PDB format	pdb6hxn.ent.gz	177.9 KB	Display	PDB format
PDBx/mmJSON format	6hxn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6hxn_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6hxn_full_validation.pdf.gz	1 MB	Display
Data in XML	6hxn_validation.xml.gz	24.1 KB	Display
Data in CIF	6hxn_validation.cif.gz	36.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hx/6hxn ftp://data.pdbj.org/pub/pdb/validation_reports/hx/6hxn	HTTPS FTP

-
Related structure data

Related structure data	6hxhC 6hxiC 6hxjC 6hxkC 6hxlC 6hxmC 6hxoC 6hxpC 6hxqC 6qclC 6qfbC C: citing same article (ref.)
Similar structure data	3d54-3 6nzy-d 6jml-2 3d54-1 6hxp-1 2zqz-1 4plz-1 2zqz-2 3gfx-d 6j9t-2 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#93 - Sep 2007 Citrate Synthase similarity (7) #154 - Oct 2012 Citric Acid Cycle similarity (12) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: ATP-citrate lyase alpha-subunit

B: ATP-citrate lyase alpha-subunit

hetero molecules

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

1

A: ATP-citrate lyase alpha-subunit

B: ATP-citrate lyase alpha-subunit

hetero molecules

A: ATP-citrate lyase alpha-subunit

B: ATP-citrate lyase alpha-subunit

hetero molecules

defined by software
Evidence: light scattering
126 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.029, 110.029, 92.749
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	ATP-citrate lyase alpha-subunit Mass: 30755.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Prior to crystallization, the N-terminal sequence MGSSHHHHHHSSGLVPR was removed by thrombin digestion. Source: (gene. exp.) Chlorobium limicola (bacteria) / Gene: aclA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q9AJC4
#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.63 Å³/Da / Density % sol: 53.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.6 M Lithium sulphate 0.1 M Tris pH 8.0 Protein Sample buffer: 20 mM HEPES pH 7.4, 150 mM NaCl

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980042 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980042 Å / Relative weight: 1
Reflection	Resolution: 1.7→50 Å / Num. obs: 71556 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 15.3 % / B_iso Wilson estimate: 25.82 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.167 / Net I/σ(I): 14.87
Reflection shell	Resolution: 1.7→1.8 Å / Redundancy: 15.4 % / Mean I/σ(I) obs: 1.64 / Num. unique obs: 11412 / CC_1/2: 0.648 / R_rim(I) all: 1.542 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
BUSTER	2.10.2	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: C. limicola ACL holoenzyme

Resolution: 1.7→34 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.945 / R_factor R_free error: 0 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.091 / SU R_free Blow DPI: 0.085 / SU R_free Cruickshank DPI: 0.082

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.192	2004	2.8 %	RANDOM
R_work	0.173	-	-	-
obs	0.173	71480	100 %	-

Displacement parameters

B_iso mean: 21.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.7752 Å²	0 Å²	0 Å²
2-	-	-1.7752 Å²	0 Å²
3-	-	-	3.5504 Å²

Refine analyze

Luzzati coordinate error obs: 0.2 Å

Refinement step

Cycle: 1 / Resolution: 1.7→34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3960	0	59	476	4495

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	4189	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.92	5703	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1461	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		95	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		637	HARMONIC	5
X-RAY DIFFRACTION	t_it		4189	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.45
X-RAY DIFFRACTION	t_other_torsion	15.53
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		549	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		5534	SEMIHARMONIC	4

LS refinement shell

Resolution: 1.7→1.74 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.245	148	2.82 %
R_work	0.258	5096	-
all	0.258	5244	-
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	0.791	-0.4074	0.4632	3.1988	0.691	1.2182	-0.064	0.0135	0.1572	0.0067	-0.0044	-0.0872	-0.0555	0.0506	0.0684	-0.055	-0.0085	-0.0153	0.0043	0.0025	0.0269	110.335	36.9763	114.801
2	0.6218	-0.227	-0.2246	0.707	0.5327	1.84	0.0475	-0.0385	-0.0776	0.0383	-0.002	-0.0724	0.0758	0.0962	-0.0455	-0.0377	0.0057	-0.017	-0.0158	0.0049	0.0243	105.9997	23.0532	114.111
3	3.1432	-1.2554	0.8341	0.6069	-1.3324	2.0014	0.0151	-0.1368	-0.1717	0.1307	-0.0385	0.0287	0.0833	0.1537	0.0235	0.0005	0.0103	-0.0092	0.0047	0.0087	0.0169	96.3313	15.8473	115.759
4	0.22	-0.3925	0.3654	1.1111	-0.1515	1.4935	0.0116	-0.0379	0.0093	-0.0135	-0.0048	0.0579	0.0412	-0.0837	-0.0067	-0.0503	-0.0074	0.0005	-0.0296	-0.0013	0.0153	81.2817	32.5868	106.235
5	0.5693	0.4344	-0.4527	1.0534	0.9462	1.7332	0.0832	-0.0377	0.1444	0.0914	-0.0248	-0.0622	-0.1615	0.0355	-0.0584	0.025	-0.0148	0.0086	0.0228	-0.0009	0.0326	85.1683	24.7386	132.245
6	0.9525	0.5934	0.4525	2.5804	1.3611	5.5135	0.0313	-0.0292	0.0524	0.0347	-0.0225	0.1167	-0.1687	-0.1337	-0.0089	-0.0667	-0.0093	0.0281	-0.0308	0.0251	0.0111	75.5242	19.6459	130.151
7	2.2803	-1.4851	0.1253	1.6759	0.3145	1.0561	-0.1182	-0.1475	-0.0377	0.2317	0.0577	-0.036	0.1455	0.0177	0.0605	-0.001	0.0023	0.0053	-0.0142	0.0319	-0.01	90.086	9.8676	121.174
8	2.3405	0.5843	-0.4042	0.9363	-0.223	0.929	-0.0416	0.0407	0.0227	0.0675	-0.0088	-0.0582	0.002	0.0298	0.0503	0.0053	-0.0076	0.0125	-0.0104	0.0089	-0.0021	82.6663	16.6496	127.183
9	1.3791	-0.3509	1.5529	1.1962	-0.5856	3.5557	-0.0346	-0.0916	-0.0265	0.0577	0.0126	0.0051	0.0367	-0.0483	0.022	-0.046	-0.0073	0.0149	-0.0414	0.0037	0.0208	87.4632	28.5062	107.677
10	0.6199	-0.3415	0.0503	0.46	-0.4118	0.1469	0.0128	0.056	-0.0756	0.0124	-0.0619	0.1869	0.0103	-0.112	0.0492	-0.0394	0.0077	-0.0009	-0.0015	-0.003	0.0554	61.8411	44.2681	102.59
11	3.866	-1.414	-0.2848	2.1762	-0.5646	1.1547	0.0263	-0.0057	-0.0217	0.0429	-0.0047	-0.2164	-0.052	0.0754	-0.0216	-0.0243	-0.0432	0.0111	-0.055	-0.0065	0.0349	94.2914	66.9545	110.561
12	1.2714	-0.0621	-0.4903	0.4686	0.1118	0.9228	-0.0349	0.0747	0.0911	0.0038	0.0213	0.041	-0.0903	-0.0341	0.0136	0.0107	-0.0009	0.004	-0.0501	0.0065	0.0154	80.7098	70.5725	106.328
13	-0.2016	0.385	0.0884	3.1285	-1.7183	1.2072	-0.0398	0.0355	0.0818	-0.0291	0.0127	0.1293	-0.1702	0.0094	0.0271	0.0246	0.0214	0.0027	-0.0066	0.008	0.0217	70.898	67.7019	99.685
14	0.0269	-0.1748	-0.1115	1.0941	-0.6362	0.7958	0.0089	-0.0078	-0.0199	-0.0196	0.0214	0.0423	0.0343	-0.0396	-0.0303	-0.033	-0.0048	0.0009	-0.0301	0.0011	0.0166	74.8533	43.7378	106.061
15	1.4165	0.3192	-0.7537	-0.0265	0.7286	2.7592	0.0357	0.0564	0.0227	-0.0011	0.0177	-0.0967	0.1129	0.1996	-0.0534	0.0001	0.0013	-0.001	0.0072	-0.0011	0.0502	80.0484	56.8587	82.6138
16	4.0483	0.4269	-1.4452	0.5981	-0.6026	2.7306	-0.0703	0.1684	-0.1819	-0.1085	0.0472	-0.0768	0.1672	0.0188	0.0231	-0.0096	-0.0005	-0.014	-0.0538	-0.0153	-0.0136	70.6958	51.2302	79.5636
17	1.0038	0.9274	-1.3955	2.9309	-0.3635	0.5476	0.0027	0.0637	0.1073	-0.0656	0.0524	0.0552	-0.0703	-0.0283	-0.0551	-0.0162	0.009	-0.0203	0.0038	0.028	-0.0085	65.6723	66.0274	91.3632
18	0.7944	0.3097	0.585	0.76	0.1974	1.1599	-0.0076	0.0393	-0.0158	-0.0057	0.0011	-0.0321	0.0535	-0.0359	0.0065	-0.0046	0.0036	-0.0075	-0.0102	0.0105	0.0189	70.5677	57.8262	84.4729
19	1.1316	1.0008	-1.1107	2.2526	-1.6966	2.5739	-0.0363	-0.0166	-0.003	-0.0873	-0.0218	0.0018	0.0369	-0.0108	0.0581	-0.0329	0.0062	-0.0102	-0.0227	-0.0026	0.0149	74.6904	51.0437	106.289
20	-0.5921	0.1249	0.2254	1.402	0.3315	0.2408	-0.0159	0.0402	-0.0995	0.0775	-0.0515	0.1235	0.0361	-0.0427	0.0674	-0.0018	-0.0079	0.0018	-0.006	-0.0033	0.03	75.0292	20.592	104.588

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|352 - A\|373 }
2	X-RAY DIFFRACTION	2	{ A\|374 - A\|398 }
3	X-RAY DIFFRACTION	3	{ A\|399 - A\|411 }
4	X-RAY DIFFRACTION	4	{ A\|412 - A\|451 }
5	X-RAY DIFFRACTION	5	{ A\|452 - A\|467 }
6	X-RAY DIFFRACTION	6	{ A\|468 - A\|500 }
7	X-RAY DIFFRACTION	7	{ A\|501 - A\|518 }
8	X-RAY DIFFRACTION	8	{ A\|519 - A\|556 }
9	X-RAY DIFFRACTION	9	{ A\|557 - A\|581 }
10	X-RAY DIFFRACTION	10	{ A\|582 - A\|607 }
11	X-RAY DIFFRACTION	11	{ B\|352 - B\|373 }
12	X-RAY DIFFRACTION	12	{ B\|374 - B\|398 }
13	X-RAY DIFFRACTION	13	{ B\|399 - B\|411 }
14	X-RAY DIFFRACTION	14	{ B\|412 - B\|451 }
15	X-RAY DIFFRACTION	15	{ B\|452 - B\|467 }
16	X-RAY DIFFRACTION	16	{ B\|468 - B\|500 }
17	X-RAY DIFFRACTION	17	{ B\|501 - B\|518 }
18	X-RAY DIFFRACTION	18	{ B\|519 - B\|556 }
19	X-RAY DIFFRACTION	19	{ B\|557 - B\|581 }
20	X-RAY DIFFRACTION	20	{ B\|582 - B\|607 }

-
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