PDB-5vt6: Crystal structure of Acetoacetyl-CoA Reductase from Burkholderia ...

ID or keywords:

Entry

Database: PDB / ID: 5vt6

Title

Crystal structure of Acetoacetyl-CoA Reductase from Burkholderia pseudomallei 1710b complexed with NADP

Components

Acetoacetyl-CoA reductase

Keywords

OXIDOREDUCTASE / SSGCID / Acetoacetyl-CoA reductase / Burkholderia pseudomallei / NADP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of Acetoacetyl-CoA Reductase from Burkholderia pseudomallei 1710b complexed with NADP
Authors: Dranow, D.M. / Davies, D.R. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	May 15, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 24, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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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Download

PDBx/mmCIF format	5vt6.cif.gz	393.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5vt6.ent.gz	318.3 KB	Display	PDB format
PDBx/mmJSON format	5vt6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5vt6_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	5vt6_full_validation.pdf.gz	1.7 MB	Display
Data in XML	5vt6_validation.xml.gz	46.5 KB	Display
Data in CIF	5vt6_validation.cif.gz	68.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vt/5vt6 ftp://data.pdbj.org/pub/pdb/validation_reports/vt/5vt6	HTTPS FTP

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Related structure data

Related structure data	3ftpS 3gk3 S: Starting model for refinement
Similar structure data	2q2q-2 3grk-2 1mfp-1 3vs8-1 5izc-d 2ewm-1 4iin-d 6t62-1 6ux3-d 6gd0-d 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: SSGCID-BupsA.00010.g

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#216 - Dec 2017 Biodegradable Plastic similarity (4) #90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#216 - Dec 2017
Biodegradable Plastic
similarity (4)
#90 - Jun 2007
Fatty Acid Synthase
similarity (3)
#77 - May 2006
Glucose Oxidase
similarity (3)
#188 - Aug 2015
Tetrahydrobiopterin Biosynthesis
similarity (2)
#134 - Feb 2011
Integrin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#194 - Feb 2016
Designer Insulins
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#259 - Jul 2021
Designed Proteins and Citizen Science
similarity (1)

Deposited unit

A: Acetoacetyl-CoA reductase

B: Acetoacetyl-CoA reductase

C: Acetoacetyl-CoA reductase

D: Acetoacetyl-CoA reductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	73.150, 92.180, 83.050
Angle α, β, γ (deg.)	90.000, 115.150, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Acetoacetyl-CoA reductase Mass: 28779.840 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria) Strain: 1710b / Gene: phbB-2, BURPS1710b_A1014 / Plasmid: BupsA.00010.g.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3JJT1, acetoacetyl-CoA reductase

#1: Protein

Acetoacetyl-CoA reductase

Mass: 28779.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: 1710b / Gene: phbB-2, BURPS1710b_A1014 / Plasmid: BupsA.00010.g.A1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3JJT1, acetoacetyl-CoA reductase

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Non-polymers , 5 types, 1030 molecules

#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₅N₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1008 / 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: 2.2 Å³/Da / Density % sol: 44.13 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 8.175 mg/mL BupsA.00010.g.A1.PS00076 in 8 mM NADP, mixed 1:1 with TOP96(h9) (10% w/v PEG8000, 0.1 M imidazole/HCl, pH = 8.0, 0.2 M calcium acetate), harvested with 20% ethylene glycol

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.1 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2017

Radiation

Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.7→39.293 Å / Num. obs: 109414 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.739 % / B_iso Wilson estimate: 14.89 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.064 / R_rim(I) all: 0.075 / Χ²: 1.042 / Net I/σ(I): 16.25 / Num. measured all: 409125 / Scaling rejects: 10

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.7-1.74	3.38	0.544	2.31	27258	8085	8064	0.748	0.649	99.7
1.74-1.79	3.745	0.436	3.05	29470	7882	7870	0.831	0.511	99.8
1.79-1.84	3.765	0.358	3.76	28782	7656	7644	0.893	0.418	99.8
1.84-1.9	3.771	0.27	4.96	27932	7419	7408	0.936	0.315	99.9
1.9-1.96	3.773	0.21	6.39	27335	7255	7244	0.961	0.246	99.8
1.96-2.03	3.78	0.164	8.16	26402	7005	6984	0.977	0.191	99.7
2.03-2.11	3.784	0.133	10.37	25376	6722	6706	0.983	0.155	99.8
2.11-2.19	3.782	0.101	13.27	24356	6452	6440	0.99	0.118	99.8
2.19-2.29	3.781	0.085	15.28	23548	6244	6228	0.993	0.099	99.7
2.29-2.4	3.795	0.074	17.47	22666	5988	5973	0.995	0.086	99.7
2.4-2.53	3.787	0.065	19.56	21366	5650	5642	0.995	0.076	99.9
2.53-2.69	3.784	0.057	21.48	20125	5335	5319	0.997	0.067	99.7
2.69-2.87	3.782	0.05	24.93	19099	5067	5050	0.997	0.058	99.7
2.87-3.1	3.772	0.041	28.87	17651	4696	4680	0.998	0.048	99.7
3.1-3.4	3.752	0.034	34.04	16139	4321	4302	0.998	0.039	99.6
3.4-3.8	3.677	0.029	38.62	14445	3942	3929	0.999	0.034	99.7
3.8-4.39	3.735	0.025	42.52	12901	3468	3454	0.999	0.029	99.6
4.39-5.38	3.746	0.024	43.57	10975	2946	2930	0.999	0.028	99.5
5.38-7.6	3.785	0.026	41.42	8618	2283	2277	0.999	0.03	99.7
7.6-39.293	3.686	0.019	46.73	4681	1299	1270	0.999	0.022	97.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3FTP

3ftp

Resolution: 1.7→39.293 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.45

	R_factor	Num. reflection	% reflection
R_free	0.1726	1865	1.7 %
R_work	0.1437	-	-
obs	0.1442	109404	99.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 70.33 Å² / B_iso mean: 19.0998 Å² / B_iso min: 7.11 Å²

Refinement step

Cycle: final / Resolution: 1.7→39.293 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7054	0	266	1024	8344
B_iso mean	-	-	19.37	31.05	-
Num. residues	-	-	-	-	956

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7566
X-RAY DIFFRACTION	f_angle_d	0.823	10245
X-RAY DIFFRACTION	f_chiral_restr	0.054	1151
X-RAY DIFFRACTION	f_plane_restr	0.005	1407
X-RAY DIFFRACTION	f_dihedral_angle_d	14.365	4527

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.7-1.7459	0.2996	112	0.2331	8245	8357
1.7459-1.7973	0.2279	135	0.1985	8239	8374
1.7973-1.8553	0.1915	161	0.1752	8235	8396
1.8553-1.9216	0.2073	152	0.1551	8261	8413
1.9216-1.9986	0.1631	130	0.1528	8251	8381
1.9986-2.0895	0.1947	142	0.1549	8275	8417
2.0895-2.1997	0.155	150	0.1363	8229	8379
2.1997-2.3375	0.1491	113	0.1335	8294	8407
2.3375-2.5179	0.1786	149	0.1387	8277	8426
2.5179-2.7713	0.1853	148	0.1448	8266	8414
2.7713-3.1721	0.1587	146	0.144	8293	8439
3.1721-3.9959	0.1658	164	0.1251	8290	8454
3.9959-39.3039	0.1537	163	0.1286	8384	8547

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	5.8449	-3.3765	-1.75	6.0626	0.7709	1.0766	-0.0091	-0.046	-0.4064	0.0345	-0.0076	0.155	0.1848	-0.0454	0.0482	0.1048	-0.0182	-0.0403	0.1115	0.0188	0.0872	34.0004	-10.1847	35.2735
2	2.067	-1.4572	-0.0929	3.3634	0.9326	0.5065	0.0267	-0.071	-0.0542	0.0152	0.0177	0.054	0.0163	-0.0349	-0.0205	0.0945	-0.009	-0.0041	0.0944	0.0193	0.086	34.0212	0.9821	32.0775
3	2.3522	0.2457	0.137	0.9777	0.1693	1.2997	0.0065	-0.3042	0.1072	0.4401	-0.0952	-0.0797	-0.2569	-0.0749	0.0712	0.2805	-0.0041	-0.0349	0.1332	0.0021	0.1019	47.7433	9.3128	53.5265
4	0.3086	0.3236	-0.2588	0.9711	-0.3291	0.7282	0.017	-0.0383	-0.0544	0.1303	-0.0297	-0.1395	-0.0379	0.0815	0.0167	0.0852	-0.0005	-0.0272	0.0902	0.006	0.1085	53.8532	5.5637	37.6146
5	1.3877	-0.6985	0.3583	3.3663	-0.7133	1.3909	0.0011	-0.0132	0.3615	0.0998	-0.0494	-0.2737	-0.2915	-0.0534	0.0732	0.1529	0.0117	0.0223	0.0998	0.003	0.1554	40.0751	16.7944	34.4294
6	0.7506	-0.3635	0.5343	2.8618	-0.7811	1.2443	-0.0183	-0.0856	-0.0294	0.1883	0.0458	0.0378	-0.0792	-0.0863	-0.0476	0.0629	-0.0048	0.0222	0.1027	-0.0008	0.0901	35.965	6.5964	36.7257
7	1.3498	-0.1079	-0.4453	1.2633	0.3187	1.4822	0.0232	0.2775	-0.0836	-0.1721	-0.0828	-0.3268	0.1092	0.4032	-0.0171	0.1213	0.0251	0.0594	0.2283	0.013	0.1924	69.3772	7.4085	5.0528
8	0.6643	-0.12	0.1113	0.8695	-0.3169	0.9807	-0.0111	0.0136	0.0334	-0.0106	-0.0391	-0.1992	-0.0434	0.1189	0.0348	0.0615	-0.009	0.004	0.1057	-0.0079	0.1234	60.2157	10.7351	19.2049
9	1.9739	-0.4782	0.1842	3.824	-1.051	2.1237	-0.0181	-0.0027	-0.1843	0.1405	-0.0152	-0.2764	0.1936	0.1923	-0.0311	0.0749	0.0196	-0.0034	0.0928	-0.0074	0.1025	54.1488	0.5076	12.8785
10	0.7722	0.0228	-0.0932	3.4451	-0.7233	0.9897	-0.0288	0.0288	-0.0425	-0.1055	0.0261	-0.1971	0.1136	0.0356	0.004	0.0639	0.0062	-0.0096	0.0953	-0.0177	0.0674	49.6197	0.6082	8.3533
11	2.9683	0.4884	-0.4477	1.2452	-0.3591	2.0662	-0.0514	0.2531	0.0433	-0.2692	0.0332	0.1346	-0.141	-0.0939	-0.0248	0.1774	0.0091	-0.0406	0.104	-0.0021	0.083	30.0849	6.2645	-10.8044
12	0.3993	-0.2659	-0.2673	0.8428	0.288	0.9557	0.0216	0.0101	-0.0495	-0.0835	0.0194	0.101	0.0244	-0.0986	-0.0311	0.091	-0.0125	-0.0183	0.0995	0.0096	0.1131	27.4546	-1.2543	4.894
13	0.3826	-0.9194	-0.2146	3.722	0.6316	0.7883	0.0101	0.0233	-0.0474	-0.0535	0.014	0.169	-0.0501	-0.0162	-0.0282	0.0686	-0.0096	-0.0002	0.1019	0.002	0.1056	37.7177	12.6795	6.7617
14	1.4418	0.7653	0.3435	3.1154	-0.0315	2.2585	0.0407	-0.1313	-0.0817	0.0262	-0.0687	0.1393	0.0336	-0.1452	0.0521	0.0866	-0.0215	0.033	0.1488	0.0344	0.1178	15.8585	-6.7362	37.6197
15	1.5967	0.5368	-0.4214	1.3093	-0.4349	2.3706	0.0465	-0.1647	-0.1433	0.1492	-0.034	0.0559	0.1543	-0.1705	-0.0426	0.1187	-0.0386	0.0228	0.1533	0.041	0.1678	10.8216	-11.7145	38.1392
16	1.0269	0.2993	-0.6561	1.2827	1.3498	5.8773	-0.0522	-0.1351	0.2152	-0.013	-0.0995	0.4115	-0.0947	-0.4376	0.1658	0.0964	0.0032	0.0017	0.2694	0.0456	0.2532	4.6864	-0.1815	29.3569
17	0.6025	-0.2263	-0.8257	1.2321	0.7648	3.1679	-0.0694	-0.0389	-0.067	-0.0032	0.0092	0.1549	0.1904	-0.0171	0.1222	0.0645	-0.0255	-0.011	0.1007	0.0167	0.1352	21.1849	-8.5654	20.7941
18	2.1937	-3.767	-3.1213	7.7882	5.7591	4.8428	-0.0262	-0.0082	-0.1343	-0.0703	-0.0388	0.2193	-0.0188	-0.1601	0.1046	0.085	-0.0256	-0.0096	0.1313	0.0283	0.1486	17.1213	-3.6555	17.388
19	4.2192	-1.1147	-0.2742	2.0408	0.7301	3.8993	-0.0249	-0.2433	0.3007	0.0463	0.1142	0.141	-0.2895	-0.2209	-0.0646	0.0715	0.003	0.0345	0.1103	0.0211	0.1205	17.0516	8.9624	32.8943
20	0.2606	0.2457	0.2871	3.6923	1.1798	1.7226	-0.0038	0.0361	-0.0072	0.1003	0.002	0.1097	0.0839	-0.0505	-0.0142	0.0549	-0.0086	0.0116	0.1077	0.0209	0.0874	27.8069	0.1871	21.2838
21	1.3958	0.1412	-0.3875	1.6972	0.8453	2.1597	0.0939	0.0639	-0.333	-0.2361	-0.1071	0.0955	0.2716	-0.0901	0.0283	0.0984	-0.023	-0.0087	0.0691	0.0019	0.1225	30.5484	-8.8744	29.1234

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 205 through 226 )	B	205 - 226
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 227 through 248 )	B	227 - 248
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 4 through 65 )	C	4 - 65
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 66 through 175 )	C	66 - 175
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 176 through 207 )	C	176 - 207
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 208 through 248 )	C	208 - 248
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 4 through 65 )	D	4 - 65
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 66 through 175 )	D	66 - 175
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 176 through 204 )	D	176 - 204
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 205 through 248 )	D	205 - 248
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 4 through 65 )	A	4 - 65
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 66 through 175 )	A	66 - 175
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 176 through 248 )	A	176 - 248
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 4 through 41 )	B	4 - 41
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 42 through 65 )	B	42 - 65
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 66 through 80 )	B	66 - 80
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 81 through 102 )	B	81 - 102
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 103 through 123 )	B	103 - 123
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 124 through 139 )	B	124 - 139
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 140 through 175 )	B	140 - 175
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 176 through 204 )	B	176 - 204

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