PDB-8wev: Crystal structure of Feruoyl-CoA Synthetase complexed with AMP fr...

ID or keywords:

Entry

Database: PDB / ID: 8wev

Title

Crystal structure of Feruoyl-CoA Synthetase complexed with AMP from Amycolatopsis thermoflava

Components

Feruloyl-CoA Synthetase

Keywords

LIGASE / Synthetase

Function / homology

Function and homology information

ligase activity, forming carbon-sulfur bonds / ATP binding
Similarity search - Function

Biological species

Amycolatopsis thermoflava N1165 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.29 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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Download

PDBx/mmCIF format	8wev.cif.gz	193.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8wev.ent.gz	151.1 KB	Display	PDB format
PDBx/mmJSON format	8wev.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/we/8wev ftp://data.pdbj.org/pub/pdb/validation_reports/we/8wev	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) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Feruloyl-CoA Synthetase

B: Feruloyl-CoA Synthetase

hetero molecules

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

1

A: Feruloyl-CoA Synthetase

B: Feruloyl-CoA Synthetase

hetero molecules

A: Feruloyl-CoA Synthetase

B: Feruloyl-CoA Synthetase

hetero molecules

defined by author&software
Evidence: gel filtration
210 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	114.764, 132.100, 161.995
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	24
Space group name H-M	I2₁2₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-628- HOH
2	1	A-642- HOH

#1: Protein	Feruloyl-CoA Synthetase Mass: 52080.277 Da / Num. of mol.: 2 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-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 58.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1%(w/v) 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 20, 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: 2.29→50 Å / Num. obs: 54605 / % possible obs: 99 % / Redundancy: 7.2 % / CC_1/2: 0.997 / CC star: 0.999 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.025 / R_rim(I) all: 0.072 / Χ²: 2.786 / Net I/σ(I): 15.9

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
2.3-2.34	4.9	0.273	2652	0.939	0.984	0.126	0.302	1.644	97.8
2.34-2.38	5.6	0.265	2691	0.94	0.984	0.115	0.291	1.762	98.4
2.38-2.43	5.8	0.247	2706	0.96	0.99	0.105	0.27	1.741	98.8
2.43-2.48	5.8	0.241	2661	0.958	0.989	0.102	0.263	1.755	98.7
2.48-2.53	6.1	0.216	2688	0.976	0.994	0.089	0.234	1.904	98.8
2.53-2.59	6.2	0.2	2741	0.975	0.994	0.081	0.217	2.014	99.2
2.59-2.66	6.4	0.183	2710	0.982	0.996	0.073	0.198	2.115	98.9
2.66-2.73	6.6	0.167	2709	0.985	0.996	0.066	0.18	2.204	99.3
2.73-2.81	6.8	0.143	2705	0.99	0.997	0.055	0.153	2.418	99.3
2.81-2.9	7.1	0.13	2712	0.992	0.998	0.049	0.139	2.535	99.3
2.9-3	7.4	0.118	2748	0.992	0.998	0.044	0.126	2.773	99.6
3-3.12	7.6	0.104	2724	0.994	0.999	0.039	0.112	3.013	99.3
3.12-3.26	7.9	0.094	2720	0.995	0.999	0.034	0.1	3.364	99.5
3.26-3.44	8.1	0.083	2762	0.997	0.999	0.03	0.088	3.547	99.4
3.44-3.65	8.3	0.075	2728	0.997	0.999	0.026	0.079	3.867	99.5
3.65-3.93	8.5	0.067	2752	0.997	0.999	0.024	0.071	3.864	99.6
3.93-4.33	8.6	0.059	2774	0.998	0.999	0.021	0.062	3.644	99.6
4.33-4.95	8.8	0.051	2792	0.998	1	0.018	0.054	3.285	99.7
4.95-6.24	8.8	0.048	2827	0.998	1	0.017	0.051	2.722	100
6.24-50	8	0.046	2803	0.997	0.999	0.017	0.049	2.884	95.7

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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: 2.29→31.49 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.918 / SU B: 7.236 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26139	2647	4.8 %	RANDOM
R_work	0.19859	-	-	-
obs	0.20151	51957	98.43 %	-

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: 53.453 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.66 Å²	0 Å²	0 Å²
2-	-	-3.09 Å²	0 Å²
3-	-	-	0.43 Å²

Refinement step

Cycle: 1 / Resolution: 2.29→31.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7198	0	50	94	7342

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	7412
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	7059
X-RAY DIFFRACTION	r_angle_refined_deg	1.534	1.642	10107
X-RAY DIFFRACTION	r_angle_other_deg	1.231	1.574	16207
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.373	5	954
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.502	19.892	370
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.928	15	1103
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.076	15	71
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	929
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8419
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1665
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	4.225	5.478	3840
X-RAY DIFFRACTION	r_mcbond_other	4.225	5.477	3839
X-RAY DIFFRACTION	r_mcangle_it	6.013	8.197	4785
X-RAY DIFFRACTION	r_mcangle_other	6.013	8.199	4786
X-RAY DIFFRACTION	r_scbond_it	4.304	5.909	3572
X-RAY DIFFRACTION	r_scbond_other	4.303	5.909	3572
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.392	8.689	5322
X-RAY DIFFRACTION	r_long_range_B_refined	8.601	63.1	7652
X-RAY DIFFRACTION	r_long_range_B_other	8.603	63.09	7645
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.292→2.351 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.327	191	-
R_work	0.268	3452	-
obs	-	-	90.35 %

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