PDB-8oxn: CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUIN...

ID or keywords:

Entry

Database: PDB / ID: 8oxn

Title

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) S101A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER NORMOXYC CONDITIONS

Components

1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase

Keywords

OXIDOREDUCTASE / ALPHA-BETA HYDROLASE / DIOXYGENASE / COFACTOR-DEVOID

Function / homology

Function and homology information

3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase / 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / catabolic process
Similarity search - Function

Biological species

Paenarthrobacter nitroguajacolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Bui, S. / Steiner, R.A.

Funding support

United Kingdom, 1items

Citation

Journal: Chem Sci / Year: 2023
Title: Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the alpha / beta-hydrolase fold.
Authors: Bui, S. / Gil-Guerrero, S. / van der Linden, P. / Carpentier, P. / Ceccarelli, M. / Jambrina, P.G. / Steiner, R.A.

History

Deposition	May 2, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8oxn.cif.gz	241.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8oxn.ent.gz		Display	PDB format
PDBx/mmJSON format	8oxn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ox/8oxn ftp://data.pdbj.org/pub/pdb/validation_reports/ox/8oxn	HTTPS FTP

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Related structure data

Related structure data	7ojmC 7okzC 8a97C 8oroC 8oxtC 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	#165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

AAA: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase

BBB: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase

CCC: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase

DDD: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase

hetero molecules

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

1

AAA: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase

hetero molecules

defined by author
Evidence: gel filtration
33.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase

hetero molecules

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

3

CCC: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase

hetero molecules

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

4

DDD: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	44.800, 167.790, 167.910
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 3 - 275 / Label seq-ID: 15 - 287

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	AAA	A
2	2	1	BBB	B
3	3	2	AAA	A
4	4	2	CCC	C
5	5	3	AAA	A
6	6	3	DDD	D
7	7	4	BBB	B
8	8	4	CCC	C
9	9	5	BBB	B
10	10	5	DDD	D
11	11	6	CCC	C
12	12	6	DDD	D

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

#1: Protein	1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase Mass: 33273.391 Da / Num. of mol.: 4 / Mutation: C69S, S101A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenarthrobacter nitroguajacolicus (bacteria) Gene: hod, meqE, ARUE_113p00080, pAL1.008 / Production host: Escherichia coli (E. coli) References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase
#2: Chemical	ChemComp-VFH / 2-methyl-quinolin-4(1H)-one Mass: 159.185 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₉NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SRT / S,R MESO-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.37 Å³/Da / Density % sol: 48.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I02 / Wavelength: 0.97949 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.5287
pseudo-merohedral	2	2	-H, -L, -K	2	0.4713

Reflection

Resolution: 2→46.56 Å / Num. obs: 86750 / % possible obs: 99.8 % / Redundancy: 7.1 % / R_merge(I) obs: 0.092 / R_pim(I) all: 0.04 / Net I/σ(I): 12.7

Reflection shell

Resolution: 2→2.05 Å / R_merge(I) obs: 0.866 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6256 / R_pim(I) all: 0.375 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→46.56 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.954 / SU B: 2.797 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.028
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1942	4298	4.96 %
R_work	0.1734	82361	-
all	0.174	-	-
obs	-	86659	99.82 %

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: 33.936 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-16.477 Å²	-0 Å²	-0 Å²
2-	-	8.801 Å²	0 Å²
3-	-	-	7.676 Å²

Refinement step

Cycle: LAST / Resolution: 2→46.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8904	0	76	158	9138

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	9333
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	8422
X-RAY DIFFRACTION	r_angle_refined_deg	1.336	1.641	12711
X-RAY DIFFRACTION	r_angle_other_deg	1.213	1.586	19416
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.615	5	1102
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.358	21.699	559
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.648	15	1467
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.281	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1118
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10900
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2248
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	1798
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	7541
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	4345
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	4000
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	217
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.14	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.401	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.351	0.2	69
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.252	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	2.662	3.488	4399
X-RAY DIFFRACTION	r_mcbond_other	2.661	3.487	4400
X-RAY DIFFRACTION	r_mcangle_it	3.745	5.218	5508
X-RAY DIFFRACTION	r_mcangle_other	3.745	5.218	5507
X-RAY DIFFRACTION	r_scbond_it	2.8	3.692	4934
X-RAY DIFFRACTION	r_scbond_other	2.8	3.692	4935
X-RAY DIFFRACTION	r_scangle_it	4.077	5.452	7203
X-RAY DIFFRACTION	r_scangle_other	4.077	5.452	7204
X-RAY DIFFRACTION	r_lrange_it	5.625	39.061	10158
X-RAY DIFFRACTION	r_lrange_other	5.624	39.059	10147
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.027	0.05	9562
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.032	0.05	9543
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.032	0.05	9554
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.034	0.05	9512
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.031	0.05	9535
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.033	0.05	9526

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.0267	0.0501
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.0267	0.0501
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.03244	0.0501
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.03244	0.0501
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.03226	0.0501
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.03226	0.0501
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.03435	0.0501
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.03435	0.0501
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.03071	0.0501
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.03071	0.0501
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.03299	0.0501
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.03299	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 (%)
2-2.052	0.298	300	0.235	5974	X-RAY DIFFRACTION	98.8343
2.052-2.108	0.264	357	0.206	5754	X-RAY DIFFRACTION	99.7063
2.108-2.169	0.273	284	0.215	5730	X-RAY DIFFRACTION	100
2.169-2.236	0.264	279	0.211	5593	X-RAY DIFFRACTION	99.8809
2.236-2.309	0.247	277	0.197	5295	X-RAY DIFFRACTION	99.9462
2.309-2.389	0.22	290	0.189	5217	X-RAY DIFFRACTION	99.9818
2.389-2.479	0.234	228	0.172	5082	X-RAY DIFFRACTION	99.9812
2.479-2.58	0.22	247	0.178	4806	X-RAY DIFFRACTION	100
2.58-2.695	0.215	213	0.188	4695	X-RAY DIFFRACTION	99.6144
2.695-2.826	0.21	228	0.191	4489	X-RAY DIFFRACTION	100
2.826-2.978	0.222	225	0.192	4262	X-RAY DIFFRACTION	99.9777
2.978-3.158	0.222	222	0.193	4000	X-RAY DIFFRACTION	99.9763
3.158-3.375	0.191	198	0.178	3784	X-RAY DIFFRACTION	99.6996
3.375-3.644	0.182	195	0.17	3560	X-RAY DIFFRACTION	99.8936
3.644-3.989	0.151	185	0.16	3254	X-RAY DIFFRACTION	99.8838
3.989-4.456	0.151	154	0.139	3015	X-RAY DIFFRACTION	99.7796
4.456-5.137	0.147	124	0.129	2662	X-RAY DIFFRACTION	99.7494
5.137-6.273	0.149	132	0.147	2268	X-RAY DIFFRACTION	99.9583
6.273-8.791	0.154	99	0.155	1824	X-RAY DIFFRACTION	99.948
8.791-46.56	0.158	61	0.173	1097	X-RAY DIFFRACTION	99.3139

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