PDB-2wya: CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 3-HYDROXY-3-METHYLGLUTAR...

ID or keywords:

Entry

Database: PDB / ID: 2wya

Title

CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 3-HYDROXY-3-METHYLGLUTARYL- COENZYME A SYNTHASE 2 (HMGCS2)

Components

HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL

Keywords

TRANSFERASE / STEROID BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS / MITOCHONDRIA / MITOCHONDRION / PHOSPHOPROTEIN / MELAVONATE PATHWAY / STEROL BIOSYNTHESIS / THIOLASE / ACETYLATION / LIPID SYNTHESIS / TRANSIT PEPTIDE / DISEASE MUTATION

Function / homology

Function and homology information

ketone body biosynthetic process / Synthesis of Ketone Bodies / hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process / cholesterol biosynthetic process / regulation of lipid metabolic process / PPARA activates gene expression / mitochondrial matrix ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Yue, W.W. / Shafqat, N. / Savitsky, P. / Roos, A.K. / Cooper, C. / Murray, J.W. / von Delft, F. / Arrowsmith, C. / Wikstrom, M. / Edwards, A. ...

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Crystal Structures of Human Hmg-Coa Synthase Isoforms Provide Insights Into Inherited Ketogenesis Disorders and Inhibitor Design.
Authors: Shafqat, N. / Turnbull, A. / Zschocke, J. / Oppermann, U. / Yue, W.W.

History

Deposition	Nov 13, 2009	Deposition site: PDBE / Processing site: PDBE
Supersession	Nov 24, 2009	ID: 2V4W
Revision 1.0	Nov 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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	2wya.cif.gz	739 KB	Display	PDBx/mmCIF format
PDB format	pdb2wya.ent.gz	612.4 KB	Display	PDB format
PDBx/mmJSON format	2wya.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wya_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	2wya_full_validation.pdf.gz	1.3 MB	Display
Data in XML	2wya_validation.xml.gz	82.3 KB	Display
Data in CIF	2wya_validation.cif.gz	119.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wy/2wya ftp://data.pdbj.org/pub/pdb/validation_reports/wy/2wya	HTTPS FTP

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Related structure data

Related structure data	2p8uSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2p8u-d 3rq1-2 4rdv-2 6b9r-2 3dxw-d 2yct-d 4emy-2 3mdw-5 4rzb-d 3rq1-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL

B: HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL

C: HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL

D: HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL

hetero molecules

209 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL

C: HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL

hetero molecules

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

2

A: HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL

D: HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL

hetero molecules

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

Unit cell

Length a, b, c (Å)	66.410, 83.514, 101.442
Angle α, β, γ (deg.)	100.00, 108.08, 96.30
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A AND (RESSEQ 49:508 )
2	1	1	CHAIN B AND (RESSEQ 49:508 )
3	1	1	CHAIN C AND (RESSEQ 49:508 )
4	1	1	CHAIN D AND (RESSEQ 49:508 )

#1: Protein	HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL / HMG-COA SYNTHASE / 3-HYDROXY-3-METHYLGLUTARYL COENZYME A SYNTHASE Mass: 51315.965 Da / Num. of mol.: 4 / Fragment: RESIDUES 51-508 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organelle: MITOCHONDRIA / Plasmid: PNH-TRXT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: P54868, hydroxymethylglutaryl-CoA synthase
#2: Chemical	ChemComp-HMG / 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / (S)-HMG-COA Mass: 906.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₉N₇O₂₀P₃S
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1457 / 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: 2.53 Å³/Da / Density % sol: 51.4 % / Description: NONE
Crystal grow	Details: 25% PEG3350, 0.1M BISTRIS PH 6.5, 0.2M AMMONIUM SULPHATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9989
Detector	Type: MARRESEARCH / Detector: CCD / Date: Aug 26, 2008
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9989 Å / Relative weight: 1
Reflection	Resolution: 1.7→35 Å / Num. obs: 212827 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / B_iso Wilson estimate: 15.36 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 7.1
Reflection shell	Resolution: 1.7→1.84 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 95.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P8U

2p8u

Resolution: 1.7→31.358 Å / SU ML: 0.19 / σ(F): 1.33 / Phase error: 17.59 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.184	3902	0.9 %
R_work	0.1614	-	-
obs	0.1616	428484	96.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 59.486 Å² / k_sol: 0.4 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.4143 Å²	-0.2111 Å²	1.4191 Å²
2-	-	2.3857 Å²	1.7399 Å²
3-	-	-	0.0286 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→31.358 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14209	0	238	1457	15904

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	14969
X-RAY DIFFRACTION	f_angle_d	1.138	20371
X-RAY DIFFRACTION	f_dihedral_angle_d	19.555	5615
X-RAY DIFFRACTION	f_chiral_restr	0.079	2225
X-RAY DIFFRACTION	f_plane_restr	0.005	2633

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3554	X-RAY DIFFRACTION	POSITIONAL
1	2	B	3554	X-RAY DIFFRACTION	POSITIONAL	0.058
1	3	C	3519	X-RAY DIFFRACTION	POSITIONAL	0.054
1	4	D	3536	X-RAY DIFFRACTION	POSITIONAL	0.064

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 (%)
1.7-1.7207	0.2868	174	0.2575	13895	X-RAY DIFFRACTION	90
1.7207-1.7425	0.2504	133	0.2404	14874	X-RAY DIFFRACTION	94
1.7425-1.7654	0.2214	120	0.2305	14912	X-RAY DIFFRACTION	96
1.7654-1.7896	0.2837	154	0.2156	15026	X-RAY DIFFRACTION	96
1.7896-1.8152	0.2347	144	0.2114	15058	X-RAY DIFFRACTION	96
1.8152-1.8423	0.2348	132	0.1949	15080	X-RAY DIFFRACTION	96
1.8423-1.8711	0.2204	134	0.1916	15009	X-RAY DIFFRACTION	96
1.8711-1.9017	0.2461	130	0.1847	15113	X-RAY DIFFRACTION	96
1.9017-1.9345	0.2072	116	0.1741	15069	X-RAY DIFFRACTION	96
1.9345-1.9697	0.1898	108	0.1685	15049	X-RAY DIFFRACTION	96
1.9697-2.0076	0.1806	147	0.1622	15165	X-RAY DIFFRACTION	97
2.0076-2.0485	0.1639	142	0.1507	15087	X-RAY DIFFRACTION	97
2.0485-2.0931	0.16	142	0.1491	15236	X-RAY DIFFRACTION	97
2.0931-2.1418	0.1657	124	0.1499	15298	X-RAY DIFFRACTION	97
2.1418-2.1953	0.1854	150	0.1476	15138	X-RAY DIFFRACTION	97
2.1953-2.2546	0.1407	128	0.1445	15159	X-RAY DIFFRACTION	97
2.2546-2.321	0.1508	154	0.1394	15198	X-RAY DIFFRACTION	97
2.321-2.3959	0.1504	140	0.1472	15291	X-RAY DIFFRACTION	98
2.3959-2.4814	0.1966	150	0.1505	15225	X-RAY DIFFRACTION	98
2.4814-2.5808	0.2037	136	0.1553	15351	X-RAY DIFFRACTION	98
2.5808-2.6982	0.1802	124	0.1546	15379	X-RAY DIFFRACTION	98
2.6982-2.8403	0.1566	150	0.1493	15318	X-RAY DIFFRACTION	98
2.8403-3.0181	0.1704	144	0.1502	15441	X-RAY DIFFRACTION	98
3.0181-3.2509	0.191	132	0.1564	15367	X-RAY DIFFRACTION	98
3.2509-3.5777	0.1753	138	0.1494	15436	X-RAY DIFFRACTION	99
3.5777-4.0944	0.1714	156	0.1361	15485	X-RAY DIFFRACTION	99
4.0944-5.1548	0.1288	153	0.1317	15512	X-RAY DIFFRACTION	99
5.1548-31.3637	0.1838	147	0.1722	15411	X-RAY DIFFRACTION	98

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	0.5131	0.0808	-0.2023	0.4737	-0.2561	0.4337	0.0057	0.0727	0.0796	0.0289	0.0309	0.0563	-0.0732	-0.053	-0.0221	0.0682	0.0015	-0.0135	0.0679	0.0006	0.0705	-12.2921	40.3885	12.5831
2	0.3539	0.2363	-0.1487	0.3486	-0.1743	0.1638	-0.0373	0.0622	-0.0427	-0.0088	0.0062	-0.0612	-0.0272	0.0739	0.012	0.0714	0.0025	-0.0147	0.0988	-0.024	0.0643	2.9594	32.7699	13.1274
3	0.6457	0.0011	0.1599	0.7883	-0.2291	0.2508	-0.0425	0.2003	0.0499	-0.0081	-0.0107	-0.1646	-0.0167	0.0858	0.0475	0.0594	-0.012	-0.0018	0.1244	0.0092	0.0806	10.2384	38.7797	4.5469
4	0.8658	0.0516	0.0016	0.4643	-0.2969	0.3273	-0.014	0.0732	0.2243	0.0643	0.0552	0.1663	-0.1567	-0.0556	-0.0493	0.1049	0.0242	0.0076	0.0606	0.016	0.1256	-15.7247	51.1439	13.9484
5	0.5414	0.2382	-0.1711	0.4643	-0.1322	0.3382	-0.024	-0.0364	-0.0695	0.059	0.0005	0.0064	-0.0162	0.034	0.0163	0.07	0.0168	0.0094	0.0603	-0.0039	0.0639	-0.9214	73.2822	-16.8503
6	0.7297	-0.02	-0.1563	0.2407	-0.1088	0.7001	-0.0538	0.0285	-0.1806	0.0142	0.0448	0.118	0.0641	-0.1284	0.0095	0.067	-0.003	0.0159	0.0692	0.0044	0.1522	-19.0299	63.6407	-20.5049
7	0.5933	0.1435	0.0217	0.4357	-0.0291	0.1709	-0.0225	-0.3326	-0.0486	0.1394	-0.0561	0.0178	-0.1182	0.0543	0.0354	0.1755	0.0294	0.0135	0.1648	0.0402	0.0976	-3.0278	68.7872	2.8765
8	0.4066	0.0865	-0.1777	0.3995	-0.0441	0.1759	0.0058	-0.2586	0.0166	0.258	-0.064	-0.0678	-0.1086	0.1952	0.0412	0.1773	-0.0186	-0.0255	0.2014	-0.0059	0.0989	9.5852	81.7155	-3.0916
9	0.5673	0.1519	-0.3033	0.3549	-0.2783	0.4145	0.0065	0.1196	0.0901	0.0112	0.0327	0.0556	-0.0709	-0.0524	-0.0137	0.077	0.0005	-0.0126	0.0869	0.0093	0.083	-0.7448	91.5091	-35.3088
10	0.4236	0.1922	-0.2643	0.2993	-0.2081	0.2554	-0.0354	0.084	-0.0001	-0.0172	0.022	-0.0261	-0.0128	0.0791	0.0022	0.0697	-0.0025	-0.0117	0.1066	-0.0232	0.0526	14.2519	84.0299	-33.7537
11	0.6647	-0.0089	0.0943	0.8484	-0.2113	0.413	-0.0422	0.2034	0.0621	-0.0366	0.0096	-0.1597	-0.0407	0.0933	0.0299	0.0698	-0.0226	0.004	0.1384	0.004	0.075	21.7579	88.9895	-43.0455
12	0.8471	0.1544	-0.0675	0.4505	-0.4159	0.5033	0.0497	0.1089	0.2793	0.0904	0.0618	0.1712	-0.1987	-0.0871	-0.0785	0.123	0.0308	0.0186	0.0866	0.0515	0.1732	-4.3153	102.1668	-35.0628
13	0.6317	0.2898	-0.0413	0.5787	-0.2465	0.2285	0.0189	-0.0921	-0.0966	0.0902	-0.0225	-0.0074	-0.0246	0.0285	0.0046	0.0758	0.0134	0.0036	0.0747	0.0038	0.0709	-9.9813	19.1698	29.7818
14	0.489	0.2061	-0.1509	0.4435	-0.2057	0.3641	-0.0057	0.0144	-0.0805	0.0043	0.0464	0.1461	0.0083	-0.0733	-0.0089	0.0693	0.0088	-0.0004	0.0759	-0.0024	0.1302	-26.872	18.5706	22.9826
15	0.0801	-0.0575	-0.0285	0.1861	-0.0588	0.225	-0.1029	-0.03	-0.3082	0.0719	0.1283	0.2147	-0.0539	-0.2846	-0.0119	0.0656	0.0047	0.0095	0.1934	0.0345	0.2439	-45.2064	13.1482	25.0077
16	0.945	0.1318	-0.0308	0.5926	-0.2973	0.507	0.025	-0.1923	-0.1745	0.118	-0.0379	0.0227	0.021	0.0365	0.003	0.0978	0.0146	0.0062	0.0895	0.0321	0.0877	-13.2444	15.2249	35.4762

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 49:204)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 205:287)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 288:424)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 425:508)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 49:257)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 258:444)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 445:460)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 461:508)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 49:205)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 206:286)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 287:424)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 425:508)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 49:205)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 206:314)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 315:362)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 363:508)

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