PDB-8weu: Crystal structure of Feruoyl-CoA Synthetase from Amycolatopsis th...

ID or keywords:

Entry

Database: PDB / ID: 8weu

Title

Crystal structure of Feruoyl-CoA Synthetase from Amycolatopsis thermoflava

Components

Fatty-acyl-CoA synthase

Keywords

LIGASE / Feruloyl-CoA Synthetase

Function / homology

Function and homology information

ligase activity, forming carbon-sulfur bonds
Similarity search - Function

Biological species

Amycolatopsis thermoflava N1165 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Seok, J. / Kim, K.-J.

Funding support

1items

Citation

Journal: To Be Published
Title: Structural analysis of feruloyl-CoA synthetase from Amycolatopsis thermoflava
Authors: Seok, J. / Kim, K.-J.

History

Deposition	Sep 18, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 25, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8weu.cif.gz	107.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8weu.ent.gz	80.4 KB	Display	PDB format
PDBx/mmJSON format	8weu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8weu_validation.pdf.gz	442.3 KB	Display	wwPDB validaton report
Full document	8weu_full_validation.pdf.gz	446.9 KB	Display
Data in XML	8weu_validation.xml.gz	22.2 KB	Display
Data in CIF	8weu_validation.cif.gz	29.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/we/8weu ftp://data.pdbj.org/pub/pdb/validation_reports/we/8weu	HTTPS FTP

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Related structure data

Similar structure data	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	#78 - Jun 2006 Luciferase similarity (6)

Deposited unit

A: Fatty-acyl-CoA synthase

hetero molecules

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

1

A: Fatty-acyl-CoA synthase

hetero molecules

A: Fatty-acyl-CoA synthase

hetero molecules

defined by author&software
Evidence: gel filtration
107 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	134.918, 134.918, 139.558
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-686- HOH
2	1	A-718- HOH

#1: Protein	Fatty-acyl-CoA synthase Mass: 53151.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis thermoflava N1165 (bacteria) Gene: EDD35_5915 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3N2H3K2
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, Ammonium sulfate, Bis-Tris

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Data collection

Diffraction

Mean temperature: 293 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 6, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 36835 / % possible obs: 97.4 % / Redundancy: 6.4 % / CC_1/2: 0.989 / CC star: 0.997 / R_merge(I) obs: 0.107 / R_pim(I) all: 0.039 / R_rim(I) all: 0.114 / Χ²: 5.337 / Net I/σ(I): 14.2 / Num. measured all: 236728

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.1-2.14	4.6	0.299	1823	0.89	0.97	0.136	0.331	1.65	97.5
2.14-2.18	4.7	0.288	1788	0.91	0.976	0.128	0.317	1.813	96
2.18-2.22	4.9	0.284	1790	0.902	0.974	0.124	0.312	2.045	96.3
2.22-2.26	5.6	0.267	1830	0.933	0.983	0.11	0.291	2.269	98.5
2.26-2.31	5	0.249	1798	0.935	0.983	0.106	0.273	2.436	95.5
2.31-2.37	5.2	0.229	1806	0.975	0.994	0.096	0.25	2.704	96.3
2.37-2.42	5.3	0.221	1787	0.955	0.989	0.092	0.241	2.589	96.6
2.42-2.49	5.5	0.214	1814	0.965	0.991	0.087	0.233	2.951	97
2.49-2.56	5.7	0.196	1788	0.968	0.992	0.078	0.212	3.687	96.1
2.56-2.65	5.8	0.181	1819	0.978	0.994	0.071	0.195	3.792	96.3
2.65-2.74	6.1	0.17	1815	0.979	0.995	0.064	0.183	4.441	96.8
2.74-2.85	6.4	0.159	1810	0.983	0.996	0.06	0.171	4.802	97.2
2.85-2.98	6.8	0.148	1838	0.985	0.996	0.054	0.158	5.788	97.3
2.98-3.14	7.1	0.137	1839	0.988	0.997	0.049	0.146	6.691	97.3
3.14-3.33	7.6	0.128	1849	0.99	0.998	0.044	0.135	7.932	98.1
3.33-3.59	7.9	0.118	1872	0.993	0.998	0.041	0.125	8.9	98
3.59-3.95	8.3	0.104	1898	0.992	0.998	0.036	0.111	9.071	99.4
3.95-4.52	8.4	0.093	1906	0.994	0.999	0.032	0.099	8.901	99.5
4.52-5.7	8.6	0.083	1930	0.995	0.999	0.029	0.088	7.2	99.4
5.7-50	8.1	0.065	2035	0.995	0.999	0.024	0.069	4.807	98.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data scaling
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→32.79 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.924 / SU B: 4.849 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25018	1874	5.1 %	RANDOM
R_work	0.19994	-	-	-
obs	0.20247	34955	97.23 %	-

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: 41.683 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.64 Å²	-0 Å²	0 Å²
2-	-	1.64 Å²	-0 Å²
3-	-	-	-3.28 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→32.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3580	0	7	126	3713

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	3680
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	3516
X-RAY DIFFRACTION	r_angle_refined_deg	1.594	1.64	5014
X-RAY DIFFRACTION	r_angle_other_deg	1.297	1.573	8078
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.472	5	480
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.247	20.055	181
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.768	15	550
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.995	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	460
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4199
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	821
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	3.444	4.272	1926
X-RAY DIFFRACTION	r_mcbond_other	3.444	4.27	1925
X-RAY DIFFRACTION	r_mcangle_it	4.93	6.393	2404
X-RAY DIFFRACTION	r_mcangle_other	4.929	6.395	2405
X-RAY DIFFRACTION	r_scbond_it	3.68	4.602	1754
X-RAY DIFFRACTION	r_scbond_other	3.678	4.603	1755
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.594	6.766	2611
X-RAY DIFFRACTION	r_long_range_B_refined	7.748	50.227	3909
X-RAY DIFFRACTION	r_long_range_B_other	7.748	50.215	3901
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.152 Å

	R_factor	Num. reflection	% reflection
R_free	0.297	134	-
R_work	0.291	2495	-
obs	-	-	94.57 %

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