PDB-7pt2: Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493Q str...

ID or keywords:

Entry

Database: PDB / ID: 7pt2

Title

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493Q structure in complex with substrate 2-HIB-CoA and inactive cofactor 3-deaza-ThDP

Components

2-hydroxyacyl-CoA lyase

Keywords

LYASE / ThDP / CoA

Function / homology

Chem-3KK / Chem-TPW

Function and homology information

Biological species

Actinomycetospora chiangmaiensis DSM 45062 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.762 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	Jun 19, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / 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	7pt2.cif.gz	781.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7pt2_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	7pt2_full_validation.pdf.gz	2.9 MB	Display
Data in XML	7pt2_validation.xml.gz	49.9 KB	Display
Data in CIF	7pt2_validation.cif.gz	76.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pt/7pt2 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/7pt2	HTTPS FTP

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Related structure data

Related structure data	7pt1C 7pt3C 7pt4C C: citing same article (ref.)
Similar structure data	7pt3-1 7pt1-1 2q27-1 2ji9-1 7pt4-1 2pgo-1 2ji8-1 2c31-1 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

Deposited unit

A: 2-hydroxyacyl-CoA lyase

B: 2-hydroxyacyl-CoA lyase

hetero molecules

133 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
267 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.674, 145.481, 174.198
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 16 - 586 / Label seq-ID: 27 - 597

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

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

#1: Protein	2-hydroxyacyl-CoA lyase Mass: 65361.168 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
#2: Chemical	ChemComp-TPW / 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE / 3-DEAZA-THDP Mass: 423.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₁₉N₃O₇P₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-3KK / S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2-hydroxy-2-methylpropanethioate / 2-Hydroxyisobutyryl-Coenzyme A Mass: 853.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₅H₄₂N₇O₁₈P₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1003 / 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: 2.51 Å³/Da / Density % sol: 51.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25% PEG 1500, 0.1 M MIB buffer pH 7.0, 5 mM 3-deazathiamin diphosphate, 1 mM 2-Hydroxybutyryl-CoA, 5 mM MgCl2, 5 mM ADP

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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: Jul 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: 1.762→87.099 Å / Num. obs: 83716 / % possible obs: 95.4 % / Redundancy: 11.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.103 / R_pim(I) all: 0.031 / Net I/σ(I): 15
Reflection shell	Resolution: 1.762→1.961 Å / Redundancy: 11.1 % / R_merge(I) obs: 1.382 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4186 / CC_1/2: 0.736 / R_pim(I) all: 0.433 / % possible all: 71.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
STARANISO		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.762→87.099 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.957 / WR_factor R_free: 0.161 / WR_factor R_work: 0.127 / SU B: 5.901 / SU ML: 0.093 / Average fsc free: 0.9292 / Average fsc work: 0.9402 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1854	4266	5.096 %
R_work	0.1466	79450	-
all	0.149	-	-
obs	-	83716	64.65 %

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: 26.748 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.106 Å²	-0 Å²	-0 Å²
2-	-	0.095 Å²	-0 Å²
3-	-	-	0.011 Å²

Refinement step

Cycle: LAST / Resolution: 1.762→87.099 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8602	0	164	1003	9769

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	8961
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	8484
X-RAY DIFFRACTION	r_angle_refined_deg	1.849	1.647	12244
X-RAY DIFFRACTION	r_angle_other_deg	1.445	1.586	19436
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.848	5	1152
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.708	20.437	504
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.824	15	1352
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.203	15	97
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1190
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	10443
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2031
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	1978
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	8624
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	4463
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	4357
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.196	0.2	878
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.098	0.2	7
X-RAY DIFFRACTION	r_metal_ion_refined	0.025	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.162	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.187	0.2	110
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.175	0.2	38
X-RAY DIFFRACTION	r_mcbond_it	1.229	2.016	4590
X-RAY DIFFRACTION	r_mcbond_other	1.228	2.016	4589
X-RAY DIFFRACTION	r_mcangle_it	1.844	3.019	5736
X-RAY DIFFRACTION	r_mcangle_other	1.844	3.019	5737
X-RAY DIFFRACTION	r_scbond_it	1.989	2.243	4369
X-RAY DIFFRACTION	r_scbond_other	1.988	2.243	4370
X-RAY DIFFRACTION	r_scangle_it	3.057	3.283	6504
X-RAY DIFFRACTION	r_scangle_other	3.057	3.283	6505
X-RAY DIFFRACTION	r_lrange_it	5.142	26.125	10331
X-RAY DIFFRACTION	r_lrange_other	4.978	25.44	10035
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.059	0.05	18391

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	0.05871	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.05871	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
1.762-1.808	0.321	9	0.282	151	0.284	9495	0.754	0.777	1.6851	0.275
1.808-1.857	0.285	25	0.252	705	0.253	9270	0.793	0.838	7.8749	0.239
1.857-1.911	0.305	59	0.223	1238	0.226	9002	0.85	0.872	14.4079	0.209
1.911-1.97	0.267	116	0.231	2336	0.233	8734	0.848	0.866	28.0742	0.213
1.97-2.034	0.257	219	0.225	3613	0.227	8503	0.866	0.875	45.0664	0.202
2.034-2.106	0.225	240	0.203	4405	0.204	8214	0.887	0.904	56.5498	0.178
2.106-2.185	0.235	250	0.193	4926	0.195	7943	0.899	0.914	65.1643	0.165
2.185-2.274	0.223	312	0.19	5476	0.192	7643	0.906	0.916	75.7294	0.154
2.274-2.375	0.234	334	0.187	6175	0.189	7314	0.9	0.919	88.9937	0.147
2.375-2.491	0.215	356	0.177	6476	0.179	7047	0.923	0.93	96.9491	0.141
2.491-2.626	0.199	349	0.162	6304	0.164	6679	0.934	0.946	99.6107	0.13
2.626-2.785	0.212	310	0.148	6006	0.152	6316	0.942	0.956	100	0.121
2.785-2.977	0.183	308	0.137	5667	0.139	5977	0.955	0.965	99.9665	0.115
2.977-3.215	0.177	288	0.14	5259	0.142	5548	0.96	0.966	99.982	0.123
3.215-3.521	0.176	256	0.139	4868	0.141	5124	0.968	0.973	100	0.129
3.521-3.936	0.169	250	0.132	4408	0.134	4658	0.969	0.977	100	0.126
3.936-4.544	0.145	192	0.11	3954	0.112	4146	0.98	0.983	100	0.107
4.544-5.561	0.143	187	0.104	3328	0.106	3515	0.979	0.985	100	0.107
5.561-7.848	0.161	124	0.129	2635	0.131	2759	0.972	0.979	100	0.131
7.848-87.099	0.164	82	0.143	1520	0.144	1605	0.974	0.974	99.8131	0.162

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	0.522	-0.11	0.0103	0.2842	0.0377	0.6645	-0.0581	0.0036	0.0827	-0.0158	-0.0175	0.0736	-0.0766	-0.0918	0.0756	0.0172	0.0107	-0.0254	0.0151	-0.0138	0.0505	-24.6642	-20.3033	32.4404
2	0.5843	-0.1172	0.0931	0.2847	0.1021	0.5176	-0.0433	0.1259	0.026	-0.06	-0.0103	-0.023	-0.0075	0.0844	0.0537	0.0242	-0.0124	0.0052	0.0471	0.0179	0.0129	7.1894	-29.465	17.4642

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	15 - 588
2	X-RAY DIFFRACTION	1	ALL	A	701
3	X-RAY DIFFRACTION	2	ALL	B	16 - 587
4	X-RAY DIFFRACTION	2	ALL	B	701

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