PDB-8s1y: ThaOS V79A

ID or keywords:

Entry

Database: PDB / ID: 8s1y

Title

ThaOS V79A

Components

8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase

Keywords

LIGASE / Alpha-oxoamine synthase / PLP / L-penicillamine / thermophilic / synthase / biocatalyst

Function / homology

Function and homology information

glycine C-acetyltransferase / glycine C-acetyltransferase activity / 8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Basle, A. / Ashley, B. / Campopiano, D.J. / Marles-wright, J.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Structure of ThAOS V79A variant with PLP-L-penicillamine thiazolidine ligand
Authors: Ashley, B. / Basle, A. / Marles-Wright, J. / Campopiano, J.D.

History

Deposition	Feb 16, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8s1y.cif.gz	333.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s1/8s1y ftp://data.pdbj.org/pub/pdb/validation_reports/s1/8s1y	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

Deposited unit

A: 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase

B: 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase

hetero molecules

94.6 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)	57.430, 63.940, 65.970
Angle α, β, γ (deg.)	64.800, 70.290, 68.180
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 395 / Label seq-ID: 27 - 420

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase / AONS/AKB ligase / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8- ...AONS/AKB ligase / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8-amino-7-ketopelargonate synthase / Alpha-oxoamine synthase / Glycine acetyltransferase Mass: 46557.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA1582 / Production host: Escherichia coli (E. coli) References: UniProt: Q5SHZ8, glycine C-acetyltransferase, 8-amino-7-oxononanoate synthase
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-A1H4V / (2~{R},4~{R})-5,5-dimethyl-2-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-1,3-thiazolidine-4-carboxylic acid Mass: 378.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₁₉N₂O₇PS / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.14 Å³/Da / Density % sol: 42.39 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: (30 mM sodium nitrate, 30 mM sodium phosphate, 30 mM ammonium sulfate, 100 mM HEPES/MOPS pH 7.5, 12.5% (w/v) PEG1000 and 12.5% (w/v) PEG3350), P21 (30 mM magnesium chloride, 30 mM calcium ...Details: (30 mM sodium nitrate, 30 mM sodium phosphate, 30 mM ammonium sulfate, 100 mM HEPES/MOPS pH 7.5, 12.5% (w/v) PEG1000 and 12.5% (w/v) PEG3350), P21 (30 mM magnesium chloride, 30 mM calcium chloride, 100 mM HEPES/MOPS pH 7.5, 12.5% (w/v) PEG1000 and 12.5% (w/v) PEG3350)

Crystal

Density Matthews: 2.14 Å³/Da / Density % sol: 42.39 %

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: (30 mM sodium nitrate, 30 mM sodium phosphate, 30 mM ammonium sulfate, 100 mM HEPES/MOPS pH 7.5, 12.5% (w/v) PEG1000 and 12.5% (w/v) PEG3350), P21 (30 mM magnesium chloride, 30 mM calcium ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9794 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.5→43.76 Å / Num. obs: 118545 / % possible obs: 96.1 % / Redundancy: 3.5 % / CC_1/2: 1 / Net I/σ(I): 15.3
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 3.5 % / Num. unique obs: 11721 / CC_1/2: 0.521

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
Aimless		data scaling
xia2		data reduction
XDS		data reduction
PHASER		phasing
MolProbity		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→43.758 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.968 / SU B: 1.553 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.192	5892	4.97 %
R_work	0.159	112653	-
all	0.161	-	-
obs	-	118545	96.063 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 24.931 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.443 Å²	0.145 Å²	0.201 Å²
2-	-	0.231 Å²	0.005 Å²
3-	-	-	0.236 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→43.758 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6137	0	96	555	6788

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	6364
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6261
X-RAY DIFFRACTION	r_angle_refined_deg	2.069	1.666	8624
X-RAY DIFFRACTION	r_angle_other_deg	0.656	1.579	14375
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.251	5	797
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.686	5	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.48	10	1087
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.324	10	272
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	977
X-RAY DIFFRACTION	r_chiral_restr_other	0.018	0.2	2
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	7440
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1418
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	1283
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	5765
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	3141
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	3582
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	434
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.023	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.254	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.231	0.2	68
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.152	0.2	35
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.028	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.471	2.377	3176
X-RAY DIFFRACTION	r_mcbond_other	2.471	2.377	3176
X-RAY DIFFRACTION	r_mcangle_it	3.087	4.266	3968
X-RAY DIFFRACTION	r_mcangle_other	3.087	4.267	3969
X-RAY DIFFRACTION	r_scbond_it	4.353	2.837	3188
X-RAY DIFFRACTION	r_scbond_other	4.353	2.837	3189
X-RAY DIFFRACTION	r_scangle_it	6.077	4.991	4653
X-RAY DIFFRACTION	r_scangle_other	6.076	4.991	4654
X-RAY DIFFRACTION	r_lrange_it	6.664	28.28	7212
X-RAY DIFFRACTION	r_lrange_other	6.664	28.279	7213
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.091	0.05	12411

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09071	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09071	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.5-1.539	0.296	426	0.282	8214	0.283	9142	0.936	0.944	94.5089	0.272
1.539-1.581	0.273	450	0.256	7986	0.257	8892	0.949	0.955	94.8718	0.24
1.581-1.627	0.277	407	0.239	7790	0.241	8625	0.952	0.962	95.0377	0.218
1.627-1.677	0.262	370	0.209	7628	0.211	8392	0.957	0.972	95.3051	0.186
1.677-1.732	0.252	360	0.198	7450	0.2	8174	0.96	0.975	95.5469	0.171
1.732-1.792	0.228	354	0.183	7192	0.186	7879	0.967	0.979	95.7736	0.157
1.792-1.86	0.247	353	0.181	6936	0.184	7571	0.963	0.98	96.2753	0.155
1.86-1.936	0.204	350	0.168	6751	0.17	7354	0.974	0.983	96.5597	0.147
1.936-2.022	0.226	323	0.168	6387	0.171	6955	0.969	0.983	96.4774	0.149
2.022-2.12	0.21	336	0.167	6155	0.169	6738	0.973	0.983	96.3342	0.153
2.12-2.234	0.203	311	0.156	5811	0.158	6356	0.974	0.985	96.3184	0.145
2.234-2.37	0.187	311	0.145	5511	0.147	6028	0.98	0.987	96.5826	0.139
2.37-2.533	0.175	261	0.155	5222	0.156	5679	0.98	0.986	96.5487	0.153
2.533-2.735	0.192	261	0.156	4853	0.158	5271	0.979	0.986	97.0214	0.159
2.735-2.995	0.209	245	0.156	4448	0.158	4832	0.976	0.986	97.1233	0.165
2.995-3.346	0.173	247	0.161	4028	0.162	4411	0.981	0.985	96.9168	0.176
3.346-3.86	0.16	185	0.153	3604	0.154	3876	0.985	0.987	97.7554	0.175
3.86-4.719	0.141	151	0.118	3054	0.119	3271	0.988	0.992	97.9823	0.148
4.719-6.635	0.198	129	0.143	2338	0.146	2532	0.983	0.99	97.4329	0.179
6.635-43.758	0.151	62	0.141	1295	0.141	1420	0.991	0.989	95.5634	0.176

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