PDB-8a97: ROOM TEMPERATURE CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-H...

ID or keywords:

Entry

Database: PDB / ID: 8a97

Title

ROOM TEMPERATURE CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) UNDER XENON PRESSURE (30 bar)

Components

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

Keywords

OXIDOREDUCTASE / ALPHA-BETA HYDROLASE /

DIOXYGENASE / COFACTOR-DEVOID /

XENON / PRESSURIZATION

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 / :
Similarity search - Function

Biological species

Paenarthrobacter nitroguajacolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.897 Å

Authors

Bui, S. / Prange, T. / 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	Jun 27, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.2	Feb 7, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8a97.cif.gz	242.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a9/8a97 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/8a97	HTTPS FTP

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Related structure data

Related structure data	7ojmC 7okzC 8oroC 8oxnC 8oxtC 2wj3S 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	#222 - Jun 2018 Proteins and Nanoparticles similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1) #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
33.6 kDa, 1 polymers

2

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

hetero molecules

defined by author
33.7 kDa, 1 polymers

3

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

hetero molecules

defined by author
33.6 kDa, 1 polymers

4

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

hetero molecules

defined by author
33.6 kDa, 1 polymers

Unit cell

Length a, b, c (Å)	44.860, 169.460, 169.310
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:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	GLN	GLN	AAA	A	1 - 274	13 - 286
2	2	1	MET	MET	GLN	GLN	BBB	B	1 - 274	13 - 286
3	3	2	MET	MET	GLY	GLY	AAA	A	1 - 275	13 - 287
4	4	2	MET	MET	GLY	GLY	CCC	C	1 - 275	13 - 287
5	5	3	THR	THR	GLN	GLN	AAA	A	2 - 274	14 - 286
6	6	3	THR	THR	GLN	GLN	DDD	D	2 - 274	14 - 286
7	7	4	MET	MET	GLN	GLN	BBB	B	1 - 274	13 - 286
8	8	4	MET	MET	GLN	GLN	CCC	C	1 - 274	13 - 286
9	9	5	THR	THR	GLN	GLN	BBB	B	2 - 274	14 - 286
10	10	5	THR	THR	GLN	GLN	DDD	D	2 - 274	14 - 286
11	11	6	THR	THR	GLN	GLN	CCC	C	2 - 274	14 - 286
12	12	6	THR	THR	GLN	GLN	DDD	D	2 - 274	14 - 286

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: 33289.391 Da / Num. of mol.: 4 / Mutation: C69S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenarthrobacter nitroguajacolicus (bacteria) Gene: hod, meqE, ARUE_113p00080, pAL1.008 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase
#2: Chemical	ChemComp-XE / XENON / Xenon Mass: 131.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₆O₆
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 49 / 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: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.42	48.22
2		48.22

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
293	1	vapor diffusion	7	PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0
293	2	vapor diffusion	7	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: 293 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 0.9686 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2012

Radiation

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

Radiation wavelength

Wavelength: 0.9686 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.5241
pseudo-merohedral	2	2	-H, -L, -K	2	0.4759

Reflection

Resolution: 2.897→53.583 Å / Num. obs: 29421 / % possible obs: 99.2 % / Redundancy: 4.4 % / B_iso Wilson estimate: 59.9 Å² / R_merge(I) obs: 0.198 / R_pim(I) all: 0.061 / Net I/σ(I): 5.4

Reflection shell

Resolution: 2.897→2.95 Å / R_merge(I) obs: 1.12 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1408 / R_pim(I) all: 0.623 / % possible all: 95.8

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2WJ3

2wj3

Resolution: 2.897→53.583 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.943 / SU B: 8.659 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2203	1483	5.047 %
R_work	0.1918	27898	-
all	0.193	-	-
obs	-	29381	98.806 %

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: 62.756 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.482 Å²	0 Å²	0 Å²
2-	-	0.271 Å²	-0 Å²
3-	-	-	-3.753 Å²

Refinement step

Cycle: LAST / Resolution: 2.897→53.583 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8966	0	54	49	9069

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	9329
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	8383
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.01	0.01	14604
X-RAY DIFFRACTION	r_angle_refined_deg	1.312	1.643	12699
X-RAY DIFFRACTION	r_angle_other_deg	1.448	1.58	19351
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.964	5	1102
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.004	21.699	559
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.172	15	1476
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.607	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	1133
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10598
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2222
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	1856
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.176	0.2	7758
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	4379
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	4266
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	158
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.208	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.269	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.059	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	2.672	6.607	4411
X-RAY DIFFRACTION	r_mcbond_other	2.672	6.606	4409
X-RAY DIFFRACTION	r_mcangle_it	4.336	9.909	5512
X-RAY DIFFRACTION	r_mcangle_other	4.336	9.909	5512
X-RAY DIFFRACTION	r_scbond_it	2.375	6.779	4918
X-RAY DIFFRACTION	r_scbond_other	2.375	6.78	4917
X-RAY DIFFRACTION	r_scangle_it	3.91	10.085	7187
X-RAY DIFFRACTION	r_scangle_other	3.91	10.085	7187
X-RAY DIFFRACTION	r_lrange_it	7.364	134.093	20139
X-RAY DIFFRACTION	r_lrange_other	7.364	134.09	20140
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.035	0.05	9606
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.027	0.05	9632
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.022	0.05	9588
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.039	0.05	9584
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.029	0.05	9588
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.032	0.05	9559

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	0.03533	0.05011
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.03533	0.05011
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.02685	0.05011
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.02685	0.05011
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.02159	0.05011
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.02159	0.05011
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.03942	0.05011
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.03942	0.05011
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.02922	0.05011
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.02922	0.05011
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.03192	0.05011
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.03192	0.05011

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 (%)
2.897-2.972	0.273	75	0.251	1972	X-RAY DIFFRACTION	93.4703
2.972-3.054	0.317	149	0.241	1917	X-RAY DIFFRACTION	99.7586
3.054-3.142	0.227	75	0.221	1952	X-RAY DIFFRACTION	99.9014
3.142-3.238	0.286	133	0.231	1883	X-RAY DIFFRACTION	100
3.238-3.344	0.247	90	0.233	1792	X-RAY DIFFRACTION	99.4189
3.344-3.461	0.213	76	0.207	1822	X-RAY DIFFRACTION	99.9473
3.461-3.591	0.275	76	0.204	1688	X-RAY DIFFRACTION	99.9433
3.591-3.737	0.272	75	0.187	1703	X-RAY DIFFRACTION	99.6078
3.737-3.902	0.198	149	0.156	1474	X-RAY DIFFRACTION	99.4485
3.902-4.092	0.156	75	0.167	1566	X-RAY DIFFRACTION	99.3943
4.092-4.312	0.21	74	0.172	1393	X-RAY DIFFRACTION	98.9211
4.312-4.571	0.174	75	0.17	1399	X-RAY DIFFRACTION	99.1258
4.571-4.884	0.209	76	0.169	1277	X-RAY DIFFRACTION	99.4853
4.884-5.272			0.165	1268	X-RAY DIFFRACTION	99.0625
5.272-5.77	0.211	71	0.194	1102	X-RAY DIFFRACTION	98.5714
5.77-6.441	0.269	74	0.215	1010	X-RAY DIFFRACTION	98.1884
6.441-7.42	0.269	72	0.218	876	X-RAY DIFFRACTION	97.8328
7.42-9.044		0	0.175	826	X-RAY DIFFRACTION	98.3333
9.044-12.612	0.172	68	0.176	578	X-RAY DIFFRACTION	97.4359
12.612-53.583			0.252	400	X-RAY DIFFRACTION	92.3788

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