PDB-6p7k: Structure of HMG-CoA reductase from Burkholderia cenocepacia

ID or keywords:

Entry

Database: PDB / ID: 6p7k

Title

Structure of HMG-CoA reductase from Burkholderia cenocepacia

Components

3-hydroxy-3-methylglutaryl coenzyme A reductase

Keywords

OXIDOREDUCTASE / HMG-CoA / mevalonate / morpheein / reductase

Function / homology

Function and homology information

hydroxymethylglutaryl-CoA reductase (NADPH) activity => GO:0004420 / hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process
Similarity search - Function

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.722 Å

Authors

Walker, A.M. / Peacock, R.B. / Hicks, C.W. / Dewing, S.M. / Lewis, K.M. / Abboud, J. / Stewart, S.W.A. / Kang, C. / Watson, J.M.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2019
Title: Structural and Functional Characterization of Dynamic Oligomerization in Burkholderia cenocepacia HMG-CoA Reductase.
Authors: Peacock, R.B. / Hicks, C.W. / Walker, A.M. / Dewing, S.M. / Lewis, K.M. / Abboud, J.C. / Stewart, S.W.A. / Kang, C. / Watson, J.M.

History

Deposition	Jun 5, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 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

-
Download

PDBx/mmCIF format	6p7k.cif.gz	229.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6p7k.ent.gz	184.1 KB	Display	PDB format
PDBx/mmJSON format	6p7k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6p7k_validation.pdf.gz	1004.2 KB	Display	wwPDB validaton report
Full document	6p7k_full_validation.pdf.gz	1006.5 KB	Display
Data in XML	6p7k_validation.xml.gz	15.6 KB	Display
Data in CIF	6p7k_validation.cif.gz	24.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p7/6p7k ftp://data.pdbj.org/pub/pdb/validation_reports/p7/6p7k	HTTPS FTP

-
Related structure data

Related structure data	6dioS S: Starting model for refinement
Similar structure data	1qay-2 1t02-2 1qax-2 1r31-2 1r7i-2 21540 4uni-d 6ptk-1 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	#96 - Dec 2007 Oxidosqualene Cyclase similarity (10) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: 3-hydroxy-3-methylglutaryl coenzyme A reductase

hetero molecules

48.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 3-hydroxy-3-methylglutaryl coenzyme A reductase

hetero molecules

x 6

defined by author&software
Evidence: light scattering
291 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_665	-y+1,x-y+1,z	1
crystal symmetry operation	3_565	-x+y,-x+1,z	1
crystal symmetry operation	10_665	-y+1,-x+1,-z+1/2	1
crystal symmetry operation	11_555	-x+y,y,-z+1/2	1
crystal symmetry operation	12_565	x,x-y+1,-z+1/2	1

Unit cell

Length a, b, c (Å)	141.485, 141.485, 122.967
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	182
Space group name H-M	P6₃22
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/2 #3: y,-x+y,z+1/2 #4: -y,x-y,z #5: -x+y,-x,z #6: x-y,-y,-z #7: -x,-x+y,-z #8: -x,-y,z+1/2 #9: y,x,-z #10: -y,-x,-z+1/2 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-724- HOH
2	1	A-1018- HOH

#1: Protein	3-hydroxy-3-methylglutaryl coenzyme A reductase / HMG-CoA reductase Mass: 47311.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: mvaA, NCTC13227_01540 / Production host: Escherichia coli (E. coli) References: UniProt: A0A2X1DZS9, hydroxymethylglutaryl-CoA reductase
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.75 Å³/Da / Density % sol: 67.24 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.2 M potassium acetate, pH 7.5, 20 g dL-1 PEG 3,350

-
Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.1 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.72→50 Å / Num. obs: 76515 / % possible obs: 99.6 % / Redundancy: 19.4 % / R_merge(I) obs: 0.114 / R_pim(I) all: 0.026 / R_rim(I) all: 0.117 / Χ²: 1 / Net I/σ(I): 8.6 / Num. measured all: 1480729

Reflection shell

Χ²: 1 / Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
1.72-1.73	6.4	1.128	1671	0.612	0.401	1.211	88.3
1.73-1.75	7.9	1.093	1855	0.622	0.363	1.163	97.5
1.75-1.77	8.9	1.043	1874	0.73	0.334	1.103	99.4
1.77-1.78	10.1	1.002	1879	0.808	0.306	1.053	99.6
1.78-1.8	11.3	1.034	1870	0.8	0.303	1.082	99.9
1.8-1.82	12.4	1.032	1902	0.857	0.29	1.075	99.9
1.82-1.83	13.6	0.966	1894	0.926	0.261	1.003	99.9
1.83-1.85	14.9	1.025	1891	0.931	0.267	1.061	100
1.85-1.87	16.5	1.116	1889	0.952	0.279	1.151	100
1.87-1.89	18.3	1.195	1880	0.946	0.285	1.229	100
1.89-1.91	20.3	0.743	1908	0.958	0.168	0.762	100
1.91-1.94	21.2	0.631	1884	0.965	0.14	0.646	100
1.94-1.96	21.7	0.785	1901	0.976	0.172	0.804	100
1.96-1.99	21.9	0.779	1893	0.978	0.169	0.797	100
1.99-2.01	22	0.583	1902	0.987	0.127	0.597	100
2.01-2.04	22.1	0.567	1903	0.987	0.123	0.581	100
2.04-2.07	22	0.466	1885	0.99	0.101	0.477	100
2.07-2.1	22.1	0.434	1897	0.991	0.094	0.444	100
2.1-2.13	22.1	0.382	1902	0.992	0.083	0.391	100
2.13-2.17	22.1	0.38	1914	0.993	0.082	0.389	100
2.17-2.2	22.1	0.374	1919	0.99	0.081	0.383	100
2.2-2.24	22.1	0.301	1892	0.992	0.065	0.308	100
2.24-2.29	22	0.288	1913	0.992	0.063	0.295	100
2.29-2.33	22.2	0.274	1900	0.995	0.059	0.28	100
2.33-2.39	22.1	0.214	1909	0.997	0.046	0.219	100
2.39-2.44	22.1	0.18	1929	0.997	0.039	0.184	100
2.44-2.5	22.1	0.152	1903	0.998	0.033	0.155	100
2.5-2.57	22.1	0.139	1935	0.998	0.03	0.142	100
2.57-2.64	22.1	0.133	1901	0.998	0.029	0.136	100
2.64-2.73	22	0.112	1946	0.999	0.024	0.114	100
2.73-2.83	22.1	0.1	1922	0.999	0.022	0.103	100
2.83-2.94	22	0.088	1926	0.999	0.019	0.09	100
2.94-3.07	21.9	0.082	1946	0.999	0.018	0.084	100
3.07-3.24	21.9	0.078	1935	0.999	0.017	0.08	100
3.24-3.44	21.9	0.073	1940	0.999	0.016	0.075	100
3.44-3.71	20.9	0.071	1966	0.999	0.016	0.073	100
3.71-4.08	19.3	0.062	1969	0.993	0.015	0.064	99.9
4.08-4.67	21.4	0.049	1986	0.996	0.011	0.05	100
4.67-5.88	21.1	0.041	2032	1	0.009	0.042	100
5.88-50	19.9	0.032	2152	0.993	0.007	0.033	99.6

-
Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6DIO

6dio

Resolution: 1.722→46.312 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1686	1811	2.59 %
R_work	0.1499	68097	-
obs	0.1504	69908	91.09 %

Solvent computation

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

Displacement parameters

B_iso max: 132.19 Å² / B_iso mean: 32.3342 Å² / B_iso min: 14.36 Å²

Refinement step

Cycle: final / Resolution: 1.722→46.312 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2768	0	118	419	3305
B_iso mean	-	-	46.61	42.8	-
Num. residues	-	-	-	-	375

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.7224-1.7689	0.2964	96	0.3188	3937	69
1.7689-1.821	0.2466	103	0.2582	4369	77
1.821-1.8798	0.2361	125	0.2211	4390	77
1.8798-1.9469	0.2415	138	0.2088	5193	91
1.9469-2.0249	0.2049	139	0.1587	5056	89
2.0249-2.1171	0.15	143	0.139	5326	94
2.1171-2.2287	0.1619	144	0.1376	5363	94
2.2287-2.3683	0.1968	147	0.157	5461	96
2.3683-2.5511	0.1666	148	0.13	5602	98
2.5511-2.8078	0.1605	152	0.1361	5689	99
2.8078-3.2141	0.1702	155	0.1382	5756	99
3.2141-4.049	0.1558	157	0.1354	5827	99
4.049-46.312	0.1416	164	0.1412	6128	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	0.1783	-0.0506	-0.1045	0.0831	-0.0266	0.1071	0.0568	0.1001	-0.0897	0.0243	-0.0052	0.069	0.1943	-0.272	0.0058	0.2626	-0.1066	-0.0356	0.3176	-0.0231	0.2442	-39.8707	48.0146	13.893
2	0.4363	0.1982	-0.0808	0.1886	0.1205	0.2478	0.0285	-0.0413	-0.0643	0.0081	-0.0007	0.0055	0.1165	-0.0724	0.0004	0.1775	-0.0316	-0.0048	0.2083	0.0017	0.1871	-21.2129	56.0054	29.0105
3	0.0651	-0.0167	0.068	0.0131	-0.0176	0.0692	0.178	-0.0159	-0.2059	0.0619	-0.056	-0.0469	0.1711	0.0151	-0	0.3003	-0.0061	-0.0669	0.2672	-0.0053	0.3266	-7.1878	47.9987	39.7544
4	0.5155	0.1343	0.0977	0.2437	0.1996	0.1784	0.0305	-0.1082	-0.0436	0.0235	0.0074	0.0042	0.0774	0.0208	-0.0015	0.1532	-0.0416	-0.0038	0.2483	-0.0123	0.1961	-11.9188	60.3326	32.7241
5	0.6061	-0.0283	-0.0781	0.1462	0.1019	0.7333	0.0205	0.0129	-0.0345	0.0105	0.001	-0.0097	0.0076	0.0381	0	0.1499	-0.0512	-0.0099	0.1953	-0.0104	0.1763	-21.0417	63.1869	20.8867

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 22 through 58 )	A	22 - 58
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 165 )	A	59 - 165
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 166 through 184 )	A	166 - 184
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 185 through 267 )	A	185 - 267
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 268 through 396 )	A	268 - 396

-
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://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