PDB-5kp8: Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthas...

ID or keywords:

Entry

Database: PDB / ID: 5kp8

Title

Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthase in Complex with Acetyl Donor-ACP

Components

CurB
CurD

Keywords

TRANSFERASE / HMG synthase / enzyme-ACP complex

Function / homology

Function and homology information

hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / acetyl-CoA metabolic process
Similarity search - Function

Biological species

Moorea producens 3L (bacteria)

Lyngbya majuscula (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.9 Å

Authors

Maloney, F.P. / Smith, J.L.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	R01-DK042303	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	R01-CA108874	United States

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Anatomy of the beta-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate.
Authors: Maloney, F.P. / Gerwick, L. / Gerwick, W.H. / Sherman, D.H. / Smith, J.L.

History

Deposition	Jul 2, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 31, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 14, 2016	Group: Database references
Revision 1.2	Sep 21, 2016	Group: Database references
Revision 1.3	Sep 20, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5kp8.cif.gz	209.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5kp8.ent.gz	166.4 KB	Display	PDB format
PDBx/mmJSON format	5kp8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5kp8_validation.pdf.gz	974.4 KB	Display	wwPDB validaton report
Full document	5kp8_full_validation.pdf.gz	977 KB	Display
Data in XML	5kp8_validation.xml.gz	21.3 KB	Display
Data in CIF	5kp8_validation.cif.gz	30.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kp/5kp8 ftp://data.pdbj.org/pub/pdb/validation_reports/kp/5kp8	HTTPS FTP

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Related structure data

Related structure data	5kp5SC 5kp6SC 5kp7C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6m20-4 1f0x-2 5kp6-d 4gc0-d 5eqh-d 6m20-1 6m20-2 5eqi-d 6jtt-2 5zhe-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (5) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: CurD

B: CurB

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	100.892, 100.892, 104.461
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	CurD / Hydroxymethylglutaryl-CoA synthase Mass: 49225.617 Da / Num. of mol.: 1 / Fragment: unp residues 17-76 / Mutation: C114S, K368A, Q369A, Q371A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorea producens 3L (bacteria) / Gene: LYNGBM3L_74540 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: F4Y432, hydroxymethylglutaryl-CoA synthase
#2: Protein	CurB Mass: 11452.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lyngbya majuscula (bacteria) / Gene: curB / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNF1
#3: Chemical	ChemComp-PNS / 4'-PHOSPHOPANTETHEINE Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₃N₂O₇PS
#4: Chemical	ChemComp-6VG / ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate Mass: 400.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₃H₂₅N₂O₈PS
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.77 Å³/Da / Density % sol: 55.62 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 6% PEG 8000, 100 mM (NH4)2SO4, 1X MMT pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2014
Radiation	Monochromator: crystal monochromator and K-B pair of biomorph mirrors Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.9→87.38 Å / Num. obs: 48869 / % possible obs: 100 % / Redundancy: 19.5 % / B_iso Wilson estimate: 29.6 Å² / R_merge(I) obs: 0.116 / Net I/σ(I): 16.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 5KP5, 5KP6

5kp5

5kp6

Resolution: 1.9→87.38 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.968 / SU B: 5.387 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.182	2374	4.9 %	RANDOM
R_work	0.157	-	-	-
obs	0.158	48869	100 %	-

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: 39.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.25 Å²	0.12 Å²	0 Å²
2-	-	0.25 Å²	0 Å²
3-	-	-	-0.81 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→87.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3805	0	45	219	4069

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	3943
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3763
X-RAY DIFFRACTION	r_angle_refined_deg	1.352	1.983	5318
X-RAY DIFFRACTION	r_angle_other_deg	0.767	3	8663
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.558	5	491
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.229	23.898	177
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.626	15	689
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.522	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	580
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4468
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	896
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	1.405	2.389	1958
X-RAY DIFFRACTION	r_mcbond_other	1.403	2.388	1957
X-RAY DIFFRACTION	r_mcangle_it	2.176	3.572	2445
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: 1.9→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.248	153	-
R_work	0.24	3396	-
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	0.391	0.202	-0.423	0.3317	-0.2744	0.5786	0.0357	-0.0943	-0.0148	0.0119	0.0334	-0.055	-0.0021	0.1964	-0.0691	0.1	0.0566	-0.023	0.2331	-0.0626	0.1494	40.5218	32.8936	13.5174
2	0.6249	0.5752	0.2187	1.4931	0.7727	0.8291	0.0577	0.0181	-0.0932	-0.0242	0.0009	-0.015	0.0976	0.0477	-0.0585	0.1505	0.0665	-0.0276	0.1194	-0.0213	0.1277	30.5693	20.5217	-5.2378
3	0.1875	-0.0884	0.0855	0.0767	-0.0595	0.4131	0.0458	-0.0032	-0.0339	0.0096	0.0437	0.0236	0.0419	0.0568	-0.0894	0.1276	0.0338	-0.0098	0.1415	-0.0076	0.1223	25.8743	30.7893	3.2657
4	0.0228	-0.0184	0.0723	0.2764	0.1182	0.9323	-0.0346	-0.0547	-0.0129	0.0974	0.1141	0.0438	0.0555	-0.012	-0.0795	0.1526	0.0825	0.0131	0.1965	0.0504	0.1172	21.199	27.2329	23.7422
5	2.5758	-0.8618	-0.3361	1.9295	0.6619	1.5966	-0.0192	-0.186	-0.0497	0.1958	0.068	0.1144	0.2493	-0.0331	-0.0487	0.1812	0.0949	0.0319	0.1799	0.0899	0.0584	24.2988	22.3461	33.9036
6	0.1894	0.0813	-0.1044	0.2173	-0.0382	0.5316	0.0024	-0.0486	-0.0312	0.0608	0.0687	0.007	0.0887	0.1226	-0.071	0.1274	0.0682	-0.0164	0.1547	0.0074	0.1166	35.3206	25.9931	13.0744
7	0.8276	-0.1505	0.1851	0.9039	0.0681	0.6206	0.0103	0.1317	-0.0555	-0.0352	0.0508	-0.0494	0.0272	0.2091	-0.0611	0.0741	0.0304	0.0267	0.2189	-0.0375	0.1096	45.8489	37.205	-5.579
8	5.4373	-3.0556	1.4068	2.3378	-1.1851	0.8853	0.046	-0.3872	0.0465	0.1214	-0.0154	0.0667	0.0019	0.0462	-0.0307	0.1694	0.0308	0.0202	0.2001	-0.0519	0.0212	21.8525	45.4266	44.1164
9	3.1479	-0.6604	3.5591	6.3681	-0.7095	4.0314	0.0327	-0.1052	-0.0072	0.2079	-0.0197	0.0684	0.0363	-0.0818	-0.013	0.0977	0.0402	0.0272	0.2346	-0.0238	0.0485	33.8743	46.0928	45.1168
10	3.4813	0.3185	-0.2481	8.6429	4.7067	2.6168	-0.1609	-0.02	0.2319	0.0455	0.315	-0.2215	0.0439	0.1592	-0.1541	0.138	0.064	-0.0215	0.1702	-0.0201	0.0695	31.4656	46.8864	34.3537
11	6.6838	1.1967	-2.9969	1.9909	-0.8724	2.8751	-0.0154	-0.185	0.1083	0.2923	0.1104	-0.1488	0.1198	-0.1914	-0.0951	0.2046	0.0482	0.0096	0.245	0.0045	0.0385	20.4246	39.0942	36.3152
12	3.1885	0.6548	1.2772	1.8731	1.3494	1.1982	-0.094	-0.3273	0.2643	-0.1163	0.0208	0.0123	-0.1032	-0.1088	0.0732	0.1604	0.1005	0.0388	0.2508	-0.0161	0.0991	17.5487	46.5058	32.4782

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 57
2	X-RAY DIFFRACTION	2	A	58 - 82
3	X-RAY DIFFRACTION	3	A	83 - 211
4	X-RAY DIFFRACTION	4	A	212 - 263
5	X-RAY DIFFRACTION	5	A	264 - 282
6	X-RAY DIFFRACTION	6	A	283 - 380
7	X-RAY DIFFRACTION	7	A	381 - 419
8	X-RAY DIFFRACTION	8	B	1 - 17
9	X-RAY DIFFRACTION	9	B	18 - 27
10	X-RAY DIFFRACTION	10	B	28 - 41
11	X-RAY DIFFRACTION	11	B	42 - 55
12	X-RAY DIFFRACTION	12	B	56 - 78

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