PDB-7pt4: Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in com...

ID or keywords:

Entry

Database: PDB / ID: 7pt4

Title

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with a covalently bound reaction intermediate as well as products formyl-CoA and acetone

Components

2-hydroxyacyl-CoA lyase

Keywords

LYASE / ThDP / CoA

Function / homology

ACETONE / Chem-FYN / Chem-OXT / THIAMINE DIPHOSPHATE

Function and homology information

Biological species

Actinomycetospora chiangmaiensis DSM 45062 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.64 Å

Authors

Zahn, M. / Rohwerder, T.

Funding support

1items

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: Mechanistic details of the actinobacterial lyase-catalyzed degradation reaction of 2-hydroxyisobutyryl-CoA.
Authors: Zahn, M. / Konig, G. / Pham, H.V.C. / Seroka, B. / Lazny, R. / Yang, G. / Ouerfelli, O. / Lotowski, Z. / Rohwerder, T.

History

Deposition	Sep 25, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 9, 2022	Group: Database references / Category: citation / Item: _citation.year
Revision 1.2	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7pt4.cif.gz	752.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7pt4_validation.pdf.gz	9.6 MB	Display	wwPDB validaton report
Full document	7pt4_full_validation.pdf.gz	9.6 MB	Display
Data in XML	7pt4_validation.xml.gz	51.5 KB	Display
Data in CIF	7pt4_validation.cif.gz	79.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pt/7pt4 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/7pt4	HTTPS FTP

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Related structure data

Related structure data	7pt1C 7pt2C 7pt3C 4rjiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7pt2-1 7pt3-1 7pt1-1 5u33-d 10915 5jc3-d 3s6p-d 3f6e-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (1)

Deposited unit

A: 2-hydroxyacyl-CoA lyase

B: 2-hydroxyacyl-CoA lyase

hetero molecules

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

1

A: 2-hydroxyacyl-CoA lyase

B: 2-hydroxyacyl-CoA lyase

hetero molecules

A: 2-hydroxyacyl-CoA lyase

B: 2-hydroxyacyl-CoA lyase

hetero molecules

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

Unit cell

Length a, b, c (Å)	116.234, 116.234, 312.056
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-716- MG
2	1	B-710- MG

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 15 - 593 / Label seq-ID: 26 - 604

Dom-ID	Component-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	2	B	B

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

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Protein , 1 types, 2 molecules AB

#1: Protein	2-hydroxyacyl-CoA lyase Mass: 65362.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinomycetospora chiangmaiensis DSM 45062 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: enoyl-CoA hydratase

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Non-polymers , 7 types, 1076 molecules

#2: Chemical	ChemComp-TPP / THIAMINE DIPHOSPHATE Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₄O₇P₂S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ACN / ACETONE Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₆O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-FYN / S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-9,13,15-TRIHYDROXY-10,10-DIMETHYL-13,15-DIOXIDO-4,8-DIOXO-12,14,16-TRIOXA-3,7-DIAZA-13,15-DIPHOSPHAHEPTADEC-1-YL} THIOFORMATE Mass: 795.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₂H₃₆N₇O₁₇P₃S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-OXT / 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1R,11R,15S,17R)-19-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-1,11,15,17-TETRAHYDROXY-12,12-DIMETHYL-15,17-DIOXIDO-6,10-DIOXO-14,16,18-TRIOXA-2-THIA-5,9-DIAZA-15,17-DIPHOSPHANONADEC-1-YL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM Mass: 1220.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₅₅N₁₁O₂₄P₅S₂ / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1049 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.33 Å³/Da / Density % sol: 47.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2 M ammonium sulfate, 0.1 M HEPES pH 7.0 1 mM 2-Hydroxyisobutyryl-CoA, 5 mM ADP, 5 mM MgCl2, 5 mM ThDP

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 11, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.64→100.662 Å / Num. obs: 98153 / % possible obs: 96.8 % / Redundancy: 40.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.189 / R_pim(I) all: 0.03 / Net I/σ(I): 15.3
Reflection shell	Resolution: 1.64→1.84 Å / Redundancy: 38.7 % / R_merge(I) obs: 1.539 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4908 / CC_1/2: 0.878 / R_pim(I) all: 0.249 / % possible all: 82.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction
xia2		data reduction
STARANISO		data scaling
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4RJI

4rji

Resolution: 1.64→100.662 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.956 / SU B: 4.341 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1751	4841	4.932 %
R_work	0.1452	93311	-
all	0.147	-	-
obs	-	98152	64.516 %

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: 19.878 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0.01 Å²	0 Å²
2-	-	0.02 Å²	-0 Å²
3-	-	-	-0.064 Å²

Refinement step

Cycle: LAST / Resolution: 1.64→100.662 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8730	0	255	1049	10034

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	9204
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	8623
X-RAY DIFFRACTION	r_angle_refined_deg	1.759	1.646	12591
X-RAY DIFFRACTION	r_angle_other_deg	1.485	1.581	19768
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.55	5	1182
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.622	20.288	520
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.047	15	1377
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.258	15	99
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	1213
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	10562
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2078
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	2042
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	8498
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	4531
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	4086
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	895
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.184	0.2	12
X-RAY DIFFRACTION	r_metal_ion_refined	0.026	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.169	0.2	46
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	188
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.14	0.2	63
X-RAY DIFFRACTION	r_mcbond_it	1.212	1.685	4675
X-RAY DIFFRACTION	r_mcbond_other	1.209	1.684	4674
X-RAY DIFFRACTION	r_mcangle_it	1.847	2.52	5844
X-RAY DIFFRACTION	r_mcangle_other	1.847	2.521	5845
X-RAY DIFFRACTION	r_scbond_it	2.538	2.074	4529
X-RAY DIFFRACTION	r_scbond_other	2.417	2.043	4494
X-RAY DIFFRACTION	r_scangle_it	3.537	3.012	6737
X-RAY DIFFRACTION	r_scangle_other	3.389	2.964	6696
X-RAY DIFFRACTION	r_lrange_it	6.071	22.208	10633
X-RAY DIFFRACTION	r_lrange_other	5.819	21.547	10343
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.076	0.05	18465

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	0.07615	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07615	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
1.64-1.683	0.185	9	0.231	207	0.229	11081	0.869	0.867	1.9493	0.221
1.683-1.729	0.319	42	0.233	850	0.237	10794	0.86	0.867	8.2639	0.219
1.729-1.779	0.258	77	0.223	1454	0.225	10516	0.853	0.885	14.5588	0.206
1.779-1.834	0.249	110	0.217	1881	0.218	10207	0.877	0.894	19.5062	0.195
1.834-1.894	0.229	141	0.203	2539	0.204	9916	0.902	0.902	27.027	0.178
1.894-1.96	0.23	190	0.2	4067	0.202	9620	0.886	0.896	44.2516	0.172
1.96-2.034	0.23	330	0.195	5919	0.197	9297	0.892	0.906	67.2152	0.167
2.034-2.117	0.213	409	0.189	8181	0.19	8959	0.916	0.918	95.8812	0.157
2.117-2.212	0.187	363	0.168	8216	0.168	8579	0.94	0.939	100	0.136
2.212-2.319	0.175	436	0.153	7790	0.154	8226	0.952	0.954	100	0.121
2.319-2.445	0.186	398	0.139	7452	0.141	7850	0.95	0.962	100	0.107
2.445-2.593	0.181	410	0.136	7035	0.138	7445	0.959	0.968	100	0.104
2.593-2.772	0.172	350	0.136	6688	0.138	7038	0.963	0.969	100	0.107
2.772-2.994	0.188	339	0.137	6219	0.14	6558	0.96	0.97	100	0.109
2.994-3.279	0.178	312	0.14	5737	0.142	6049	0.965	0.972	100	0.118
3.279-3.666	0.151	245	0.13	5287	0.131	5532	0.975	0.98	100	0.114
3.666-4.232	0.133	246	0.116	4661	0.117	4907	0.981	0.984	100	0.104
4.232-5.181	0.123	176	0.111	4034	0.112	4210	0.983	0.986	100	0.1
5.181-7.317	0.176	167	0.149	3188	0.15	3355	0.972	0.976	100	0.131
7.317-100.662	0.191	91	0.169	1906	0.17	1997	0.964	0.968	100	0.166

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	0.1314	-0.0461	0.0252	0.0613	-0.0134	0.0155	0.0245	0.0098	0.0317	-0.0174	-0.0229	-0.0156	0.0073	0.011	-0.0016	0.0141	0.0002	0.009	0.0178	-0.0026	0.0129	-18.1266	-36.1116	21.4145
2	0.1502	-0.0545	0.0486	0.035	-0.005	0.0791	0.0216	0.0074	0.0306	-0.0137	-0.0077	-0.0113	-0.0066	-0.0015	-0.0139	0.0224	0.0003	0.0111	0.0034	0.0029	0.0161	-55.6772	-20.2871	12.8864

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	15 - 594
2	X-RAY DIFFRACTION	1	ALL	A	701 - 717
3	X-RAY DIFFRACTION	2	ALL	B	15 - 598
4	X-RAY DIFFRACTION	2	ALL	B	701 - 710

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