PDB-3psz: Crystal Structure of AhQnr, the Qnr protein from Aeromonas hydrop...

ID or keywords:

Entry

Database: PDB / ID: 3psz

Title

Crystal Structure of AhQnr, the Qnr protein from Aeromonas hydrophila (P21212 crystal form)

Components

Qnr

Keywords

CELL CYCLE / pentapeptide repeat / antibiotic resistance / Type II DNA topoisomerase

Function / homology

Function and homology information

: / Pentapeptide repeats (8 copies) / E3 ubiquitin-protein ligase SopA / Pentapeptide repeat / Pectate Lyase C-like / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology

Biological species

Aeromonas hydrophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Xiong, X. / Spencer, J.

Citation

Journal: Nucleic Acids Res. / Year: 2011
Title: Structural insights into quinolone antibiotic resistance mediated by pentapeptide repeat proteins: conserved surface loops direct the activity of a Qnr protein from a Gram-negative bacterium
Authors: Xiong, X. / Bromley, E.H.C. / Oelschlaeger, P. / Woolfson, D.N. / Spencer, J.

History

Deposition	Dec 2, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jan 26, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3psz.cif.gz	195.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3psz.ent.gz	157.7 KB	Display	PDB format
PDBx/mmJSON format	3psz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3psz_validation.pdf.gz	468.1 KB	Display	wwPDB validaton report
Full document	3psz_full_validation.pdf.gz	471.1 KB	Display
Data in XML	3psz_validation.xml.gz	20.5 KB	Display
Data in CIF	3psz_validation.cif.gz	29.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ps/3psz ftp://data.pdbj.org/pub/pdb/validation_reports/ps/3psz	HTTPS FTP

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Related structure data

Related structure data	3pssSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5dns-1 2xtx-d 5dns-2 3pss-d 2v05-d 6fls-1 6fls-2 2w7z-d 4dhx-1 4x36-d 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: Qnr

B: Qnr

hetero molecules

50.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	88.730, 116.290, 55.100
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 6 / Auth seq-ID: 1 - 216 / Label seq-ID: 1 - 216

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

#1: Protein	Qnr Mass: 24493.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Strain: hydrophila ATCC 7966 / Gene: AHA_0291 / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0KF03
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.61 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1M sodium cacodylate, 1.5M sodium acetate, 20mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2008
Radiation	Monochromator: double crystal Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.117 Å / Relative weight: 1
Reflection	Resolution: 2.2→43.43 Å / Num. all: 29576 / Num. obs: 28777 / % possible obs: 98.1 % / Redundancy: 4.4 % / B_iso Wilson estimate: 22.162 Å² / R_merge(I) obs: 0.132 / Net I/σ(I): 8
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.424 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4050 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PSS

3pss

Resolution: 2.2→41.45 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.915 / SU B: 13.361 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2699	1455	5.1 %	RANDOM
R_work	0.21085	-	-	-
obs	0.21379	27321	97.33 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 16.51 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.16 Å²	-0 Å²	0 Å²
2-	-	-2.51 Å²	-0 Å²
3-	-	-	0.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→41.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3394	0	91	249	3734

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	3538
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2348
X-RAY DIFFRACTION	r_angle_refined_deg	1.364	1.977	4767
X-RAY DIFFRACTION	r_angle_other_deg	0.845	3	5677
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.324	5	438
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.941	24.974	195
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.931	15	579
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.721	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	496
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4052
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	752
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	0.466	1.5	2165
X-RAY DIFFRACTION	r_mcbond_other	0.123	1.5	900
X-RAY DIFFRACTION	r_mcangle_it	0.852	2	3402
X-RAY DIFFRACTION	r_scbond_it	1.588	3	1373
X-RAY DIFFRACTION	r_scangle_it	2.5	4.5	1361
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 2841 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
LOOSE POSITIONAL	0.39	5
LOOSE THERMAL	0.88	10

LS refinement shell

Resolution: 2.204→2.261 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.281	111	-
R_work	0.256	2007	-
obs	-	-	98.74 %

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	19.0614	1.5366	1.0615	4.5384	-1.9608	1.6552	-0.3363	0.0677	0.4071	0.0922	0.0991	-0.334	-0.1786	0.3003	0.2371	0.29	-0.0115	-0.0597	0.1536	0.0039	0.1537	-27.2864	65.2303	-7.5323
2	74.3656	-31.1872	4.9855	11.4203	-2.6174	-2.574	0.5306	1.0294	0.9622	-0.4989	-0.4439	-0.801	0.0826	0.4367	-0.0867	0.6025	0.2524	0.2548	0.4751	0.0089	0.6457	-30.3022	65.495	-17.7072
3	3.8706	-0.2789	3.1579	1.7297	0.7549	4.0252	0.0337	0.2805	0.1054	-0.3118	0.0146	-0.2349	-0.1126	0.3057	-0.0483	0.1308	0.0221	-0.0142	0.0565	0.0209	0.1261	-29.0963	59.1225	-12.0995
4	3.2044	-0.0094	1.3554	2.4495	0.1272	3.4323	-0.0506	-0.0606	0.0039	-0.0932	0.0016	0.036	-0.1333	-0.109	0.049	0.0436	0.0046	-0.0003	0.0026	0.0025	0.0369	-30.3618	50.7036	-9.4909
5	6.4804	-4.299	-9.1997	2.3976	5.1507	10.7568	0.096	0.9768	-0.4761	-0.2322	-0.6479	0.4957	-0.1734	-1.2201	0.5519	0.3553	0.0664	-0.1821	0.2681	-0.1123	0.4924	-31.9535	38.8308	-26.7946
6	4.1783	0.558	0.1936	2.8634	1.6006	5.3762	0.0147	-0.0136	-0.0494	-0.086	0.0228	0.1027	-0.0102	-0.0835	-0.0375	0.028	0.0072	0.0051	0.0016	0.0114	0.0283	-29.8804	39.2258	-13.0661
7	3.7349	0.1205	-0.0177	2.2015	0.4887	1.4909	-0.0616	-0.1782	-0.0279	0.1001	-0.0098	0.097	0.039	-0.0903	0.0714	0.0264	0.0118	-0.0039	0.0285	0.0121	0.0432	-32.2132	33.7314	-11.9776
8	4.9163	0.6494	-2.097	2.4984	-2.0526	3.1363	0.0597	-0.5082	-0.0628	0.1604	-0.0392	0.0679	0.0258	0.0937	-0.0206	0.0765	0.0101	-0.0001	0.0954	-0.028	0.1141	-29.9308	26.4709	-10.9162
9	1.6961	-0.9937	0.422	7.4954	-3.5458	3.9971	0.152	-0.1409	0.0089	0.2555	-0.0973	0.0769	0.0892	-0.0487	-0.0547	0.0835	-0.0139	0.0023	0.0684	-0.0295	0.0155	-26.5418	15.6644	-11.6608
10	14.8188	2.0744	-1.4168	4.2135	0.1139	5.8245	-0.1371	0.1389	-0.3242	-0.2143	0.126	-0.3106	0.481	0.1427	0.0111	0.2836	0.0263	0.0692	0.019	-0.0368	0.2182	-28.312	-38.8847	-20.3272
11	28.6108	-9.4174	20.5614	1.2423	-6.9674	7.214	0.3336	0.5702	-0.6925	0.1566	-0.0098	0.0225	0.027	0.7179	-0.3237	0.6017	-0.0784	0.0504	0.4484	-0.2048	0.4111	-31.1021	-39.395	-9.9606
12	3.385	0.3856	-2.1976	2.6062	-0.5897	4.1561	-0.1064	-0.1	-0.1444	0.031	-0.0252	-0.0768	0.3295	0.0457	0.1316	0.0713	-0.0092	0.0188	0.0204	-0.0099	0.0986	-30.4839	-30.2809	-18.5007
13	2.8323	0.7727	-0.5002	2.2947	0.0732	4.6499	-0.0502	-0.062	0.0729	0.0788	0.005	0.0871	0.1609	-0.1173	0.0453	0.0426	-0.0027	0.0085	0.0079	-0.0064	0.0488	-30.7756	-21.8941	-16.3386
14	9.2328	6.4795	12.4367	4.2602	8.7551	15.8468	-0.0592	-1.1886	0.6711	0.0782	-0.8607	0.5755	0.1684	-1.5419	0.9199	0.3478	-0.0796	0.0541	0.236	-0.0043	0.3816	-32.5081	-12.6154	-0.5892
15	3.8614	0.1864	-0.3576	3.2223	2.2585	4.6801	-0.0026	0.0097	0.0624	0.0022	0.0456	0.1249	-0.1414	0.0044	-0.043	0.0096	-0.0046	-0.0057	0.0057	0.02	0.0361	-30.3391	-12.9487	-14.4507
16	3.3897	0.5494	0.3531	3.7905	0.8858	3.1529	-0.0545	0.0424	0.0488	-0.1785	-0.0436	0.3198	-0.1512	-0.1369	0.0982	0.0117	0.0055	-0.0169	0.0276	0.0199	0.0502	-32.6474	-7.4528	-15.4485
17	3.6626	-1.0162	0.5277	3.3037	-0.5182	2.9775	0.2165	0.3583	-0.0642	-0.2459	-0.1727	0.2026	-0.1003	-0.1178	-0.0438	0.0748	-0.0078	0.008	0.1048	-0.0254	0.0959	-31.2825	1.4192	-15.5754
18	1.0701	-3.2617	1.104	10.972	-5.8842	5.8054	0.0322	0.094	0.0052	-0.2485	-0.3012	-0.3386	0.1235	0.167	0.269	0.0832	0.0009	0.0433	0.0623	-0.0191	0.1263	-23.3427	12.1717	-17.5183

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 13
2	X-RAY DIFFRACTION	2	A	14 - 20
3	X-RAY DIFFRACTION	3	A	21 - 41
4	X-RAY DIFFRACTION	4	A	42 - 100
5	X-RAY DIFFRACTION	5	A	101 - 114
6	X-RAY DIFFRACTION	6	A	115 - 142
7	X-RAY DIFFRACTION	7	A	143 - 160
8	X-RAY DIFFRACTION	8	A	161 - 188
9	X-RAY DIFFRACTION	9	A	189 - 216
10	X-RAY DIFFRACTION	10	B	1 - 13
11	X-RAY DIFFRACTION	11	B	14 - 20
12	X-RAY DIFFRACTION	12	B	21 - 65
13	X-RAY DIFFRACTION	13	B	66 - 100
14	X-RAY DIFFRACTION	14	B	101 - 114
15	X-RAY DIFFRACTION	15	B	115 - 142
16	X-RAY DIFFRACTION	16	B	143 - 160
17	X-RAY DIFFRACTION	17	B	161 - 196
18	X-RAY DIFFRACTION	18	B	197 - 216

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