PDB-8aut: WelO5* L221A bound to Zn(II), Cl, 2-oxoglutarate, and 12-epi-hapa...

ID or keywords:

Entry

Database: PDB / ID: 8aut

Title

WelO5* L221A bound to Zn(II), Cl, 2-oxoglutarate, and 12-epi-hapalindole C

Components

Oxidoreductase

Keywords

OXIDOREDUCTASE / WelO5* 2-oxoglutarate-dependent halogenase / 12-epi-hapalindole C

Function / homology

: / Carrier-protein-independent halogenase WelO5 / metal ion binding / 2-OXOGLUTARIC ACID / Chem-OAU / Oxidoreductase

Function and homology information

Biological species

Hapalosiphon welwitschii UH IC-52-3 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.685 Å

Authors

Buller, R. / Hueppi, S. / Voss, M. / Schaub, D.

Funding support

Switzerland, 1items

Citation

Journal: Chemcatchem / Year: 2022
Title: Enzyme engineering enables inversion of substrate stereopreference of the halogenase WelO5*
Authors: Voss, M. / Huppi, S. / Schaub, D. / Hayashi, T. / Ligibel, M. / Sager, E. / Schroer, K. / Snajdrova, R. / Buller, R.M.U.

History

Deposition	Aug 25, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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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Download

PDBx/mmCIF format	8aut.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8aut.ent.gz	725.5 KB	Display	PDB format
PDBx/mmJSON format	8aut.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8aut_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	8aut_full_validation.pdf.gz	2.7 MB	Display
Data in XML	8aut_validation.xml.gz	42.8 KB	Display
Data in CIF	8aut_validation.cif.gz	56.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/au/8aut ftp://data.pdbj.org/pub/pdb/validation_reports/au/8aut	HTTPS FTP

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Related structure data

Related structure data	8acvSC S: Starting model for refinement C: citing same article (ref.)
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	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1)

Deposited unit

A: Oxidoreductase

B: Oxidoreductase

C: Oxidoreductase

D: Oxidoreductase

hetero molecules

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

1

A: Oxidoreductase

hetero molecules

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

2

B: Oxidoreductase

hetero molecules

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

3

C: Oxidoreductase

hetero molecules

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

4

D: Oxidoreductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	106.458, 106.458, 385.220
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 11 - 290 / Label seq-ID: 31 - 310

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Oxidoreductase Mass: 34569.875 Da / Num. of mol.: 4 / Mutation: L221A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hapalosiphon welwitschii UH IC-52-3 (bacteria) Gene: welO15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A075X7C6

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Non-polymers , 7 types, 130 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-AKG / 2-OXOGLUTARIC ACID Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₆O₅ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-OAU / 3-[(1~{S},2~{R},3~{S},6~{S})-3-ethenyl-2-isocyano-3-methyl-6-prop-1-en-2-yl-cyclohexyl]-1~{H}-indole / 12-epi-hapalindole C isoniltrile / 3-[(1R,2S,3R,6R)-3-ethenyl-2-isocyano-3-methyl-6-prop-1-en-2-ylcyclohexyl]-1H-indole Mass: 304.429 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₄N₂ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.41 Å³/Da / Density % sol: 49.1 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% PEG-4000, 200 mM LiSO4, in 100 mM TRIS pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000009 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 8, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.000009 Å / Relative weight: 1
Reflection	Resolution: 2.68→49.17 Å / Num. obs: 37222 / % possible obs: 99.9 % / Redundancy: 38.9 % / B_iso Wilson estimate: 67.52 Å² / CC_1/2: 1 / Net I/σ(I): 16.7
Reflection shell	Resolution: 2.68→2.8 Å / Num. unique obs: 4433 / CC_1/2: 0.782

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8ACV

8acv

Resolution: 2.685→49.17 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.954 / SU B: 34.206 / SU ML: 0.305 / Cross valid method: FREE R-VALUE / ESU R Free: 0.319
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2315	1862	5.003 %	RANDOM
R_work	0.186	35359	-	-
all	0.188	-	-	-
obs	-	37221	99.847 %	-

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: 90.612 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.883 Å²	0.942 Å²	0 Å²
2-	-	1.883 Å²	0 Å²
3-	-	-	-6.109 Å²

Refinement step

Cycle: LAST / Resolution: 2.685→49.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8690	0	161	110	8961

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	9049
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8094
X-RAY DIFFRACTION	r_angle_refined_deg	1.435	1.65	12258
X-RAY DIFFRACTION	r_angle_other_deg	0.459	1.559	18888
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.462	5	1092
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.829	5	56
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	4.41	10	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.031	10	1473
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.728	10	434
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	1313
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10324
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1828
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	1925
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.197	0.2	8006
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	4502
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	4804
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	202
X-RAY DIFFRACTION	r_metal_ion_refined	0.111	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.099	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	65
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.28	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	4.492	5.408	4395
X-RAY DIFFRACTION	r_mcbond_other	4.491	5.408	4395
X-RAY DIFFRACTION	r_mcangle_it	6.505	8.1	5478
X-RAY DIFFRACTION	r_mcangle_other	6.505	8.099	5479
X-RAY DIFFRACTION	r_scbond_it	5.396	5.906	4654
X-RAY DIFFRACTION	r_scbond_other	5.328	5.894	4643
X-RAY DIFFRACTION	r_scangle_it	7.83	8.693	6780
X-RAY DIFFRACTION	r_scangle_other	7.785	8.677	6763
X-RAY DIFFRACTION	r_lrange_it	9.78	68.285	10016
X-RAY DIFFRACTION	r_lrange_other	9.78	68.293	10017
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.083	0.05	9030
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.084	0.05	9040
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.078	0.05	9081
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.082	0.05	9077
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.081	0.05	9033
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.079	0.05	9078

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	0.08326	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08326	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08379	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08379	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07781	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07781	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0817	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0817	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08149	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.08149	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07911	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07911	0.0501

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.685-2.754	0.367	133	0.373	2513	X-RAY DIFFRACTION	99.1754
2.754-2.83	0.342	130	0.324	2483	X-RAY DIFFRACTION	99.9235
2.83-2.911	0.307	128	0.299	2411	X-RAY DIFFRACTION	99.9213
2.911-3.001	0.318	124	0.264	2356	X-RAY DIFFRACTION	100
3.001-3.099	0.266	120	0.23	2274	X-RAY DIFFRACTION	99.75
3.099-3.207	0.27	117	0.203	2229	X-RAY DIFFRACTION	100
3.207-3.328	0.255	113	0.19	2148	X-RAY DIFFRACTION	100
3.328-3.463	0.257	109	0.203	2055	X-RAY DIFFRACTION	99.7695
3.463-3.616	0.209	104	0.184	1989	X-RAY DIFFRACTION	99.9522
3.616-3.791	0.269	101	0.186	1912	X-RAY DIFFRACTION	99.9007
3.791-3.995	0.243	96	0.168	1810	X-RAY DIFFRACTION	99.7906
3.995-4.236	0.19	91	0.152	1740	X-RAY DIFFRACTION	100
4.236-4.526	0.184	85	0.132	1627	X-RAY DIFFRACTION	100
4.526-4.885	0.178	81	0.143	1544	X-RAY DIFFRACTION	100
4.885-5.346	0.145	76	0.148	1431	X-RAY DIFFRACTION	99.9337
5.346-5.968	0.244	68	0.169	1304	X-RAY DIFFRACTION	100
5.968-6.875	0.284	62	0.194	1167	X-RAY DIFFRACTION	100
6.875-8.379	0.26	54	0.172	1010	X-RAY DIFFRACTION	99.9061
8.379-11.682	0.167	43	0.152	823	X-RAY DIFFRACTION	100
11.682-49.17	0.281	27	0.242	533	X-RAY DIFFRACTION	100

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	3.9288	1.9758	-0.0464	2.1421	0.601	3.4316	-0.1566	0.5992	-0.1301	0.1954	0.3447	-0.1056	0.0741	0.6177	-0.1881	0.186	0.1583	0.0998	0.5134	0.1093	0.1049	-5.0631	38.5312	-29.1593
2	3.1148	1.6025	0.2546	1.5699	1.2067	3.1335	-0.0666	-0.0182	0.2936	-0.135	-0.1943	0.1992	-0.2814	-0.1198	0.2609	0.4322	0.1658	-0.0619	0.1326	0.0704	0.4047	-23.2791	68.9377	-1.9624
3	3.0654	0.9738	0.6711	1.5323	-0.4734	3.731	-0.2923	-0.0785	0.3214	0.1335	-0.017	0.1814	-0.2801	-0.5166	0.3093	0.3155	0.1269	0.0117	0.191	-0.0503	0.4297	-51.7782	54.6961	-25.7759
4	3.8244	1.8673	0.8151	2.8956	0.1876	3.9152	0.4566	-0.0099	-0.0559	0.4598	-0.3653	-0.0473	0.961	-0.11	-0.0912	0.6418	0.0051	0.1651	0.0902	0.0533	0.11	-31.7284	20.8725	-5.438

Refinement TLS group

Selection: ALL

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