PDB-6d0p: 1.88 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxy...

ID or keywords:

Entry

Database: PDB / ID: 6d0p

Title

1.88 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii

Components

Pirin family protein

Keywords

OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Quercetin 2 / 3-dioxygenase

Function / homology

Function and homology information

quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / metal ion binding
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.88 Å

Authors

Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: 1.88 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A.

History

Deposition	Apr 10, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 25, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6d0p.cif.gz	506.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6d0p.ent.gz	419.8 KB	Display	PDB format
PDBx/mmJSON format	6d0p.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d0/6d0p ftp://data.pdbj.org/pub/pdb/validation_reports/d0/6d0p	HTTPS FTP

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Related structure data

Similar structure data	5uto-1 3vn2-d 6fzf-2 3b1m-d 6i9c-d 6cng-1 6fzf-1 2p54-d 6dj6-2 3fej-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP95893

Similar structure data

Other databases

TargetTrack: CSGID-IDP95893

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pirin family protein

B: Pirin family protein

C: Pirin family protein

D: Pirin family protein

hetero molecules

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

1

A: Pirin family protein

hetero molecules

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

2

B: Pirin family protein

hetero molecules

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

3

C: Pirin family protein

hetero molecules

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

4

D: Pirin family protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	95.481, 131.977, 123.987
Angle α, β, γ (deg.)	90.00, 103.58, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-414- HOH
2	1	B-402- HOH
3	1	D-424- HOH

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Pirin family protein / Quercetin 2 / 3-dioxygenase Mass: 32480.059 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: A7N09_17085, B4R90_18685, B9X95_09530, BGC29_11425, BWP00_02730, CPI82_04080, CV950_06630, CV954_00950, IX87_13390 Plasmid: pMCSG73 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: A0A0C0C2K2

#1: Protein

Pirin family protein / Quercetin 2 / 3-dioxygenase

Mass: 32480.059 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acinetobacter baumannii (bacteria)
Gene: A7N09_17085, B4R90_18685, B9X95_09530, BGC29_11425, BWP00_02730, CPI82_04080, CV950_06630, CV954_00950, IX87_13390
Plasmid: pMCSG73 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: A0A0C0C2K2

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Non-polymers , 9 types, 1075 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#8: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1056 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.86 Å³/Da / Density % sol: 57 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 8.5 mg/mL protein in 0.01 M Tris, pH 8.3, screen: Classics II (H1) (0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 8.5, 25% w/v PEG3350)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 14, 2018 / Details: C(111)
Radiation	Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.88→30 Å / Num. obs: 120737 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / B_iso Wilson estimate: 24.4 Å² / R_merge(I) obs: 0.094 / R_pim(I) all: 0.05 / R_rim(I) all: 0.107 / R_sym value: 0.094 / Χ²: 1.216 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.88→1.91 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.763 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6014 / CC_1/2: 0.649 / R_pim(I) all: 0.404 / R_rim(I) all: 0.865 / R_sym value: 0.763 / Χ²: 1.004 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0222	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.88→29.81 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.954 / SU B: 5.034 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19039	5945	4.9 %	RANDOM
R_work	0.15821	-	-	-
obs	0.15975	114778	99.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 27.715 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	0 Å²	-0.41 Å²
2-	-	0.33 Å²	0 Å²
3-	-	-	-0.15 Å²

Refinement step

Cycle: 1 / Resolution: 1.88→29.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8912	0	101	1056	10069

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.015	9970
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	8844
X-RAY DIFFRACTION	r_angle_refined_deg	1.34	1.775	13575
X-RAY DIFFRACTION	r_angle_other_deg	0.432	1.79	20750
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.323	5	1291
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.251	21.128	337
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.89	15	1213
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.707	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	1228
X-RAY DIFFRACTION	r_gen_planes_refined	0.02	0.021	11528
X-RAY DIFFRACTION	r_gen_planes_other	0.017	0.02	1956
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.384	1.626	4966
X-RAY DIFFRACTION	r_mcbond_other	1.383	1.625	4964
X-RAY DIFFRACTION	r_mcangle_it	2.081	2.427	6302
X-RAY DIFFRACTION	r_mcangle_other	2.081	2.427	6303
X-RAY DIFFRACTION	r_scbond_it	2.428	2.001	5004
X-RAY DIFFRACTION	r_scbond_other	2.428	2.001	5004
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.772	2.838	7267
X-RAY DIFFRACTION	r_long_range_B_refined	6.436	22.47	10330
X-RAY DIFFRACTION	r_long_range_B_other	6.285	21.658	10072
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free	21.502	5	2
X-RAY DIFFRACTION	r_sphericity_bonded	31.152	5	2

LS refinement shell

Resolution: 1.88→1.929 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.268	425	-
R_work	0.239	8328	-
obs	-	-	98.63 %

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	0.4861	-0.1123	-0.3302	0.5309	-0.1959	1.6169	-0.0148	-0.0198	0.0566	0.0364	0.0636	-0.0005	0.0124	0.0527	-0.0488	0.0066	-0.0065	0.0088	0.072	-0.0042	0.0743	-25.7814	-11.9737	63.6549
2	0.4947	-0.1995	-0.1247	0.5165	-0.1647	0.6718	-0.0078	0.0072	-0.0445	0.046	0.0397	0.0748	0.0016	-0.0639	-0.0318	0.0107	-0.0097	0.0097	0.0407	0.0187	0.0798	-40.6178	-10.8172	63.3509
3	1.2095	-0.4815	-0.0553	0.8916	-0.0486	0.4457	0.0089	0.04	-0.0805	-0.0824	0.0232	0.0369	0.0663	0.0101	-0.0322	0.0204	-0.0134	0.0038	0.0517	-0.0167	0.0641	-28.1346	-17.5301	52.0133
4	0.15	0.4983	-0.1281	3.7013	1.5487	2.8694	0.0554	-0.0762	0.077	0.0217	0.0915	-0.03	-0.24	0.2898	-0.1469	0.1328	-0.0047	0.0252	0.1685	-0.0478	0.2543	-35.7594	11.2431	63.6703
5	2.0386	0.0047	-0.1408	0.5512	-0.0854	0.566	-0.0683	0.2228	0.0306	0.059	0.1121	0.0061	-0.0467	-0.0183	-0.0437	0.0295	0.0168	-0.0019	0.0648	-0.0214	0.0667	-20.6604	21.3686	70.2845
6	1.7477	-0.6971	0.0275	1.9305	-0.1291	0.3729	-0.0711	-0.1461	-0.0166	0.2422	0.0901	0.1047	-0.0789	-0.0679	-0.019	0.0817	0.0508	0.0266	0.0553	-0.0029	0.0385	-29.3389	18.5655	84.2826
7	1.3354	0.5893	-0.2777	1.3132	-0.4187	1.0992	-0.0002	-0.0325	0.1081	0.2319	0.0267	-0.1298	-0.2337	0.0359	-0.0265	0.0831	0.0091	-0.0323	0.0417	-0.0433	0.0793	-11.5561	25.7372	78.3146
8	1.6337	1.2062	0.8507	6.504	1.9058	0.7702	0.0459	0.1681	-0.2177	0.3104	-0.0028	-0.0789	0.083	-0.0009	-0.0431	0.1149	-0.0073	0.0104	0.1478	-0.0633	0.169	-22.4301	-2.1304	79.8267
9	0.9159	0.3181	0.1247	1.6718	0.0842	0.9613	-0.1144	0.1002	0.0084	-0.2345	0.1027	0.0648	-0.0109	0.0385	0.0117	0.0846	-0.0275	-0.0019	0.0478	0.0376	0.0411	-55.6475	12.1618	32.7855
10	0.9808	0.1448	0.2504	0.9212	-0.0842	0.6755	-0.0571	0.0864	-0.1749	-0.0618	0.07	0.1101	0.1014	-0.0213	-0.0129	0.0417	-0.0169	0.0118	0.028	0.0114	0.0873	-58.9975	-4.1648	37.7809
11	3.5783	-2.0909	-0.0076	3.2241	0.6958	1.1003	-0.0514	-0.0987	0.0944	0.2227	-0.016	0.0745	-0.0868	-0.091	0.0674	0.071	0.0139	0.0308	0.0623	0.0239	0.0476	-59.7308	11.5208	51.3478
12	1.4384	-0.5953	0.0135	2.1203	0.1044	0.8011	-0.0198	0.1027	0.0023	-0.1509	0.0036	0.0122	-0.0252	0.0283	0.0161	0.079	-0.0211	0.0226	0.0547	0.027	0.0333	-51.2465	11.1777	38.1615
13	2.3687	1.1676	0.4527	1.8944	0.5926	1.5383	0.0726	0.0072	-0.0371	-0.1067	0.1149	0.0179	0.1025	-0.0251	-0.1876	0.1493	-0.0421	-0.0327	0.0773	0.0539	0.0569	-52.3816	28.663	26.203
14	0.7299	0.1414	0.4342	1.3396	0.7054	2.4781	0.0016	0.013	0.0407	-0.1588	0.0782	-0.0361	-0.1852	0.2442	-0.0798	0.1299	-0.0284	0.0135	0.0641	0.0068	0.0155	-43.0786	39.554	19.5122
15	1.4147	0.2775	-0.2413	0.9282	-0.1509	2.2316	0.0704	-0.0259	0.0071	-0.182	0.0543	0.2066	-0.0105	-0.302	-0.1247	0.1431	-0.0124	-0.0533	0.0889	0.0487	0.0639	-58.5276	32.6996	15.6998
16	3.6327	1.9112	0.2694	7.7715	2.1321	1.3505	0.1618	-0.2358	-0.5452	-0.2183	0.0541	-0.94	0.2352	0.4049	-0.2159	0.1624	0.116	0.0217	0.2443	0.0076	0.1541	-30.1906	25.0834	10.0759

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 53
2	X-RAY DIFFRACTION	2	A	54 - 160
3	X-RAY DIFFRACTION	3	A	161 - 264
4	X-RAY DIFFRACTION	4	A	265 - 287
5	X-RAY DIFFRACTION	5	B	0 - 53
6	X-RAY DIFFRACTION	6	B	54 - 121
7	X-RAY DIFFRACTION	7	B	122 - 264
8	X-RAY DIFFRACTION	8	B	265 - 287
9	X-RAY DIFFRACTION	9	C	0 - 46
10	X-RAY DIFFRACTION	10	C	47 - 150
11	X-RAY DIFFRACTION	11	C	151 - 192
12	X-RAY DIFFRACTION	12	C	193 - 287
13	X-RAY DIFFRACTION	13	D	0 - 27
14	X-RAY DIFFRACTION	14	D	28 - 121
15	X-RAY DIFFRACTION	15	D	122 - 264
16	X-RAY DIFFRACTION	16	D	265 - 287

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-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 9 types, 1075 molecules

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-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Download

-
Validation report

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Related structure data

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Links

-
Assembly

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Components

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Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 9 types, 1075 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi