PDB-2wgv: Crystal structure of the OXA-10 V117T mutant at pH 6.5 inhibited ...

ID or keywords:

Entry

Database: PDB / ID: 2wgv

Title

Crystal structure of the OXA-10 V117T mutant at pH 6.5 inhibited by a chloride ion

Components

BETA-LACTAMASE OXA-10

Keywords

HYDROLASE / ANTIBIOTIC RESISTANCE / PLASMID ENCODED

Function / homology

Function and homology information

penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / plasma membrane
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Vercheval, L. / Kerff, F. / Bauvois, C. / Sauvage, E. / Guiet, R. / Charlier, P. / Galleni, M.

Citation

Journal: Biochem.J. / Year: 2010
Title: Three Factors that Modulate the Activity of Class D Beta-Lactamases and Interfere with the Post- Translational Carboxylation of Lys70.
Authors: Vercheval, L. / Bauvois, C. / Di Paolo, A. / Borel, F. / Ferrer, J.L. / Sauvage, E. / Matagne, A. / Frere, J.M. / Charlier, P. / Galleni, M. / Kerff, F.

History

Deposition	Apr 27, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	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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Download

PDBx/mmCIF format	2wgv.cif.gz	119.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2wgv.ent.gz	93.7 KB	Display	PDB format
PDBx/mmJSON format	2wgv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wgv_validation.pdf.gz	471.2 KB	Display	wwPDB validaton report
Full document	2wgv_full_validation.pdf.gz	475.2 KB	Display
Data in XML	2wgv_validation.xml.gz	23.9 KB	Display
Data in CIF	2wgv_validation.cif.gz	34.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wg/2wgv ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wgv	HTTPS FTP

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Related structure data

Related structure data	2wgwC 2wkhC 2wkiC 1k4fS 1e3u 1e4d 1ewz 1fof 1k4e 1k54 1k55 1k56 1k57 1k6r 1k6s 2wgi S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5mnu-d 2x02-d 2x01-d 1k6s-d 6skq-2 6skp-d 5fq9-d 1k57-2 2hpb-d 1k4f-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: BETA-LACTAMASE OXA-10

B: BETA-LACTAMASE OXA-10

hetero molecules

56.2 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)	48.750, 101.700, 126.600
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	BETA-LACTAMASE OXA-10 / BETA-LACTAMASE PSE-2 Mass: 27714.512 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET 22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase

#1: Protein

BETA-LACTAMASE OXA-10 / BETA-LACTAMASE PSE-2

Mass: 27714.512 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET 22B / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase

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Non-polymers , 5 types, 363 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H₂O

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Details

Compound details	ENGINEERED RESIDUE IN CHAIN A, VAL 117 TO THR ENGINEERED RESIDUE IN CHAIN B, VAL 117 TO THR
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: 2.59 Å³/Da / Density % sol: 52.14 % / Description: NONE
Crystal grow	pH: 6.5 / Details: 1.8 M AS BUFFER, CITRATE 0.1 M PH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979742
Detector	Type: ADSC CCD / Detector: CCD / Date: Jul 26, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979742 Å / Relative weight: 1
Reflection	Resolution: 1.8→47.19 Å / Num. obs: 59000 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / B_iso Wilson estimate: 25.25 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 15.2
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 5.8 % / R_merge(I) obs: 1.24 / Mean I/σ(I) obs: 1.6 / % possible all: 97

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
SCALA		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4F

1k4f

Resolution: 1.8→47.19 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.953 / SU B: 5.606 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20909	2979	5.1 %	RANDOM
R_work	0.18212	-	-	-
obs	0.18354	55922	99.46 %	-

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: 23.821 Å²

	B_aniso -1	B_aniso -2
1-	0.01 Å²	0 Å²
2-	-	-0.01 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.8→47.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3890	0	41	353	4284

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	4058
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.262	1.953	5495
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.398	5	510
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.763	25.056	178
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.815	15	733
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.62	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	601
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3021
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	1842
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.297	0.2	2820
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	297
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	0.274	0.2	15
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.147	0.2	11
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	0.591	1.5	2570
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.935	2	4002
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.513	3	1746
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.4	4.5	1483
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	179	-
R_work	0.292	3877	-
obs	-	-	94.86 %

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	19.9395	-1.509	13.4532	2.3281	-3.0125	10.8735	-0.1484	0.9026	1.3758	-0.3127	-0.4545	-0.3359	-0.283	0.8172	0.6029	0.1775	0.0273	0.0792	0.1596	0.0901	0.0819	24.084	51.695	42.865
2	0.7055	0.1398	-0.9892	1.188	-0.8087	2.8165	0.0395	0.1075	0.0381	-0.075	-0.047	0.0159	-0.1034	-0.0533	0.0075	-0.0111	0.0102	-0.0116	-0.0126	0.0289	0.0295	16.529	42.11	53.889
3	11.2033	-7.0019	-1.2378	5.8295	1.5217	4.7446	-0.5371	-0.4534	0.0967	0.4791	0.4493	-0.0994	0.1404	0.1875	0.0878	-0.0022	0.0334	0.0059	-0.0705	-0.0139	-0.0228	20.89	32.549	76.936
4	2.7078	0.3532	0.6265	0.9108	0.1301	1.2688	-0.0288	-0.0158	-0.0811	0.0728	0.1015	0.029	0.0495	0.0125	-0.0726	-0.0065	0.0143	0.0113	-0.0209	0.0162	0.0213	14.099	32.182	69.009
5	1.0333	-0.0787	-0.2254	1.6421	0.2054	1.6278	0.02	0.0469	0.0378	-0.0384	0.0103	0.0808	-0.1706	-0.086	-0.0303	-0.0152	0.0174	0.0028	-0.0325	0.0249	0.0212	10.977	40.521	59.899
6	4.2114	-5.1397	-1.1706	7.8521	1.0297	2.459	0.1974	0.2045	0.0771	-0.2266	-0.223	-0.1162	-0.1259	0.0706	0.0257	-0.0017	-0.0041	0.007	-0.0233	0.0168	0.0322	23.55	41.048	55.561
7	4.2762	-3.8425	-0.264	4.9525	-0.0229	1.8696	0.0896	0.078	0.2268	-0.0581	-0.1073	-0.2022	-0.292	0.1456	0.0177	0.022	-0.0247	0.0143	-0.0534	0.0292	0.0232	24.191	46.115	54.562
8	2.9356	-4.3102	0.9535	10.9601	-1.2317	0.6236	0.0521	-0.0396	0.4288	0.0667	-0.0594	-0.5792	-0.3129	0.2446	0.0074	0.0452	-0.0656	0.0445	-0.008	0.0236	0.1022	27.01	53.362	54.43
9	11.7794	6.1953	-8.2577	12.3964	-8.3013	7.5034	0.2081	-0.3501	-0.3119	0.5405	-0.1255	-1.1053	-0.3356	1.4187	-0.0827	0.1866	-0.0771	0.0008	0.3041	-0.1861	-0.0182	22.136	58.286	99.037
10	0.8587	-0.5511	-0.4514	1.0128	0.2621	3.8893	0.197	-0.0737	0.2429	-0.0326	0.0176	0.0299	-0.5851	0.1558	-0.2146	0.1262	-0.0166	0.0956	-0.0925	-0.0609	0.0296	11.078	60.868	90.015
11	9.0968	0.7081	-4.7837	1.6628	-3.2115	7.5294	0.3103	0.26	0.8208	-0.3666	-0.2139	0.2329	-1.0306	-0.4958	-0.0964	0.5719	0.2324	0.0274	0.1221	0.0576	0.2625	1.571	66.309	65.147
12	17.8992	-8.6227	-2.5698	56.8741	2.0286	38.0071	-0.7314	-1.0003	1.2881	0.3047	0.6537	-1.1368	-1.0706	2.2636	0.0777	0.463	-0.0584	0.0874	0.2181	0.0136	0.4819	12.265	75.93	68.307
13	4.7103	0.3268	-2.7693	0.9017	0.6405	2.5139	0.2859	0.0558	0.4073	-0.2136	-0.0313	0.1012	-1.0313	-0.3775	-0.2546	0.5379	0.1952	0.0604	0.1135	0.0306	0.2211	2.347	67.737	73.094
14	1.3049	-0.4542	-0.3577	1.6636	1.0409	3.567	0.1692	-0.0347	0.1461	-0.1109	-0.0595	0.1265	-0.5491	-0.2712	-0.1097	0.147	0.0814	0.0655	-0.0718	-0.0106	0.0274	4.914	59.713	83.026
15	1.6288	-0.4684	-0.7225	10.9734	3.0141	4.2053	0.2722	-0.153	0.3555	-0.1506	0.0082	-0.2162	-0.7789	0.3234	-0.2804	0.1727	-0.0917	0.1416	-0.0393	-0.0861	0.0366	16.624	63.519	87.944
16	3.1351	-5.4643	0.5395	18.8104	-0.9509	3.1596	0.1074	-0.0699	0.4583	-0.661	0.3718	-1.2054	-0.6712	0.9318	-0.4792	0.0566	-0.165	0.1654	0.0976	-0.1718	0.0261	25.099	61.054	87.525

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	20 - 33
2	X-RAY DIFFRACTION	2	A	34 - 83
3	X-RAY DIFFRACTION	3	A	84 - 104
4	X-RAY DIFFRACTION	4	A	105 - 133
5	X-RAY DIFFRACTION	5	A	134 - 205
6	X-RAY DIFFRACTION	6	A	206 - 229
7	X-RAY DIFFRACTION	7	A	230 - 248
8	X-RAY DIFFRACTION	8	A	249 - 264
9	X-RAY DIFFRACTION	9	B	19 - 34
10	X-RAY DIFFRACTION	10	B	35 - 79
11	X-RAY DIFFRACTION	11	B	80 - 95
12	X-RAY DIFFRACTION	12	B	96 - 104
13	X-RAY DIFFRACTION	13	B	105 - 131
14	X-RAY DIFFRACTION	14	B	132 - 210
15	X-RAY DIFFRACTION	15	B	211 - 245
16	X-RAY DIFFRACTION	16	B	246 - 264

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