PDB-2x01: CRYSTAL STRUCTURE OF THE OXA-10 S67A MUTANT AT PH 7

ID or keywords:

Entry

Database: PDB / ID: 2x01

Title

CRYSTAL STRUCTURE OF THE OXA-10 S67A MUTANT AT PH 7

Components

BETA-LACTAMASE OXA-10

Keywords

HYDROLASE / ANTIBIOTIC RESISTANCE

Function / homology

Function and homology information

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

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

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

Citation

Journal: To be Published
Title: Evidence of Chloride Inhibition and Impact of the Hydrophobic Core on the Lysine Carboxylated in Class D Beta-Lactamase
Authors: Vercheval, L. / Kerff, F. / Bauvois, C. / Sauvage, E. / Guiet, R. / Borel, F. / Ferrer, J.L. / Charlier, P. / Galleni, M.

History

Deposition	Dec 4, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 8, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 20, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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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PDBx/mmCIF format	2x01.cif.gz	217.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2x01.ent.gz	174.4 KB	Display	PDB format
PDBx/mmJSON format	2x01.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2x01_validation.pdf.gz	476.5 KB	Display	wwPDB validaton report
Full document	2x01_full_validation.pdf.gz	486.1 KB	Display
Data in XML	2x01_validation.xml.gz	23.1 KB	Display
Data in CIF	2x01_validation.cif.gz	31.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/2x01 ftp://data.pdbj.org/pub/pdb/validation_reports/x0/2x01	HTTPS FTP

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Related structure data

Related structure data	1k4fS 1e3u 1e4d 1ewz 1fof 1k4e 1k54 1k55 1k56 1k57 1k6r 1k6s 2wgi 2wgv 2wgw 2wkh 2wki 2x02 S: Starting model for refinement
Similar structure data	2hpb-d 1k55-2 1k57-2 4wz5-2 5fq9-d 1k56-2 1ewz-2 5mmy-d 3lce-1 5mnu-d 1e4d-1 1k57-1 1fof-d 2x02-d 2wgv-d 6skp-d 5mox-d 3lce-2 2hp6-d 1k55-1 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

56.8 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)	48.376, 95.071, 125.562
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	BETA-LACTAMASE OXA-10 / BETA-LACTAMASE PSE-2 Mass: 27739.541 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
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, SER 67 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 67 TO ALA
Sequence details	LYS 70 AND KCX (LYSINE NZ-CARBOXYLIC ACID) 70 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. IN ...LYS 70 AND KCX (LYSINE NZ-CARBOXYLIC ACID) 70 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. IN CHAIN A AND B, THE STRUCTURE WAS MODELLED AS A MIXTURE OF CARBONATED AND UNCARBONATED FORM.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.2 % / Description: NONE
Crystal grow	pH: 7 / Details: 1.8M AS, 0.1M HEPES, PEG 400 50%, DMSO, PH 7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97967
Detector	Type: ADSC CCD / Detector: CCD / Date: Jul 11, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97967 Å / Relative weight: 1
Reflection	Resolution: 1.9→48.39 Å / Num. obs: 45383 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / B_iso Wilson estimate: 23.81 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 14.4
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 7.6 % / R_merge(I) obs: 0.96 / Mean I/σ(I) obs: 2.5 / % possible all: 96.9

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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: 1.9→29.81 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.909 / SU B: 9.323 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.267	2307	5.1 %	RANDOM
R_work	0.213	-	-	-
obs	0.216	43022	97.5 %	-

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: 29.037 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.07 Å²	0 Å²	0 Å²
2-	-	-0.04 Å²	0 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→29.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3896	0	66	181	4143

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	4036
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.517	1.959	5454
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.781	5	494
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.213	25.196	179
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.401	15	723
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.738	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	594
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2974
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	1981
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	2790
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	211
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	0.221	0.2	28
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.125	0.2	9
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	2.493	2	2525
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.227	3	3945
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.814	2	1755
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.672	3	1506
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: 1.9→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.345	180	-
R_work	0.274	3075	-
obs	-	-	96.39 %

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	29.3713	1.3404	14.9297	4.005	2.4772	14.5091	-0.7921	-1.7488	1.6372	-0.5429	-0.4326	0.6912	-0.9235	-0.9256	1.2247	0.2616	0.1603	-0.1683	0.0753	-0.2124	0.2148	6.6726	5.479	81.2801
2	39.6504	3.1328	-13.1899	3.4753	2.554	8.3941	0.5058	-0.8585	2.1901	-0.5512	-0.5938	0.827	-0.6261	-0.4345	0.0879	0.1494	0.1784	-0.0908	0.4075	-0.2471	0.3453	-4.8481	1.5645	78.8668
3	8.602	4.4414	-4.29	4.1837	-0.2295	6.3532	-0.3366	0.0234	0.4128	0.0954	0.1147	-0.0395	-0.6691	-0.098	0.2218	0.1307	0.1094	-0.1901	0.0052	-0.072	0.0662	6.8479	1.4556	74.8061
4	0.9521	0.6518	1.607	1.8297	2.2581	3.6815	-0.2768	-0.147	0.2609	0.3298	0.1799	-0.1224	-0.0687	0.1083	0.0969	0.1224	0.0992	-0.1087	0.0817	-0.0972	0.0615	8.645	-4.9187	79.2723
5	0.0492	0.1316	-0.4538	0.3521	-1.2145	4.1892	-0.6861	-1.0859	0.3376	0.8094	0.428	-0.2653	-0.1996	0.1017	0.2581	-0.0082	0.039	-0.0827	-0.0235	-0.0151	0.0598	9.8271	-13.6622	63.6134
6	3.4634	-0.9394	0.1307	0.6417	0.5904	1.3072	-0.1774	0.0665	0.2269	0.0075	-0.088	-0.3189	-0.091	0.361	0.2654	0.0348	-0.0406	-0.0434	0.0436	0.0458	0.0443	19.7991	-13.1163	54.2484
7	5.1607	2.5691	-1.0814	3.652	-0.4138	3.6047	-0.4004	0.3357	-0.0184	-0.0917	0.1862	-0.1302	0.308	-0.1767	0.2142	0.0316	-0.0553	-0.0149	0.0429	0.0234	-0.051	5.098	-18.4982	48.5853
8	2.269	-0.2467	0.7602	0.7381	-0.629	1.1772	-0.2188	0.1141	0.046	0.0667	0.0846	-0.0258	-0.0584	0.0944	0.1342	0.0257	-0.0261	-0.0265	0.0217	-0.004	-0.0204	14.1078	-18.3716	57.6623
9	1.2069	-0.0543	0.0678	0.7509	-0.2432	1.1723	-0.1683	-0.1149	0.2117	0.151	0.0237	-0.0367	-0.1377	0.103	0.1446	0.0584	0.0128	-0.0847	0.0167	-0.0159	0.0178	17.5408	-10.7198	65.438
10	2.4638	1.063	-1.364	2.0325	-2.2287	4.0526	-0.1363	-0.1512	0.2665	0.0761	0.0012	0.005	-0.3988	-0.0867	0.1352	0.079	0.0591	-0.1141	-0.025	-0.0448	0.012	4.7375	-3.4396	64.7461
11	1.8894	0.7834	-1.0807	3.5277	-1.6139	1.761	-0.0677	-0.0324	0.264	0.187	0.1388	0.2679	-0.4405	-0.2166	-0.0711	0.0876	0.0781	-0.1077	0.0362	-0.0471	0.0132	2.4933	-3.4813	69.6484
12	8.6271	4.0572	0.8449	12.5557	2.6546	3.6364	-0.6838	-0.1167	1.2996	-0.3716	0.212	1.2023	-0.8309	-0.3099	0.4719	0.213	0.1333	-0.239	-0.0043	-0.0311	0.1697	-0.6378	3.5819	68.3893
13	1.1259	-0.8015	-0.3175	11.815	-0.4762	4.5903	0.1355	0.0126	-0.0839	-1.1822	-0.139	1.3737	-0.3055	-0.8198	0.0036	-0.0779	0.0828	-0.0966	0.1656	0.103	0.066	-0.9219	6.7699	25.7526
14	0.0587	0.4534	-0.3138	4.3241	-1.3093	3.1926	0.1792	0.0767	0.1252	-0.5437	-0.2652	-0.1187	0.176	-0.1544	0.086	-0.0213	0.086	0.0539	0.0669	0.1216	0.0159	7.3667	3.6925	26.9002
15	1.9959	-0.9843	1.4589	0.9921	-0.8511	4.2397	0.0353	0.0328	0.2824	0.1817	-0.0905	-0.4866	-0.5321	0.2111	0.0551	0.054	-0.0626	-0.0049	-0.0142	0.1052	0.2055	19.4063	13.7767	39.9531
16	7.0334	-2.3028	-2.0283	1.9078	1.6002	3.6471	0.0346	-0.0091	1.2228	0.17	-0.1821	-0.4973	-0.8855	0.335	0.1474	0.3734	-0.1516	-0.1917	-0.0003	0.025	0.3541	19.6319	19.8824	54.4777
17	5.9378	3.1706	2.7691	9.0896	-0.1085	7.6054	-0.1146	-0.4058	0.5109	0.0691	-0.0455	0.0766	-0.6334	-0.4656	0.1601	0.2603	-0.0327	-0.2905	-0.1334	0.0042	0.2077	13.9754	18.1421	53.4967
18	4.6282	-0.0475	-1.5389	1.7356	0.5565	7.7404	0.0504	-0.0754	0.4958	0.1635	-0.1775	-0.2692	-0.9218	0.6674	0.1272	0.0588	-0.1277	-0.0919	-0.0558	0.1301	0.228	25.0156	17.6633	42.3831
19	3.2519	0.0659	0.6944	1.4073	-0.4138	3.1952	0.0159	0.2605	0.4966	0.1066	-0.2139	-0.5037	-0.8161	0.4844	0.198	0.0907	-0.0872	0.0339	0.0572	0.1835	0.2891	21.0163	16.7758	32.5933
20	1.7234	-1.2288	0.6977	2.4911	-1.3698	6.3265	0.044	0.1225	0.0795	0.2906	-0.2483	-0.4353	-0.1249	0.3674	0.2043	-0.0718	-0.0529	-0.0365	0.0036	0.124	0.1614	20.2842	1.4426	41.9174
21	0.2566	1.043	-1.12	8.826	-3.4074	5.1738	-0.0272	0.033	0.2242	0.1788	0.1671	-0.0151	-0.1579	-0.4717	-0.1399	0.0271	-0.0081	-0.0558	0.0116	0.084	0.0271	6.4161	7.51	44.2408
22	1.1785	0.0892	-0.0652	6.4939	-4.1431	4.2507	0.0755	0.0659	0.1789	0.2901	-0.0218	0.0798	-0.3943	-0.2793	-0.0537	0.01	0.0227	0.0324	0.0458	0.0957	0.0505	6.1261	10.8474	34.6635
23	8.5165	-3.5159	-1.0402	21.2908	2.0111	5.5907	0.0209	0.1847	0.2777	0.8826	-0.0744	0.7303	-0.7	-0.8295	0.0535	-0.0176	0.1085	0.1171	0.1296	0.0768	0.0352	-1.5842	13.8987	36.9838
24	7.5604	-0.1118	-2.8458	31.2365	-5.6135	12.3709	0.0164	0.1796	-0.7054	1.3595	0.4226	3.4914	0.4101	-0.896	-0.439	-0.0584	-0.0474	0.2254	0.1252	0.0923	0.4527	-2.9437	0.1851	36.5454

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 28
2	X-RAY DIFFRACTION	2	A	29 - 34
3	X-RAY DIFFRACTION	3	A	35 - 49
4	X-RAY DIFFRACTION	4	A	50 - 64
5	X-RAY DIFFRACTION	5	A	65 - 70
6	X-RAY DIFFRACTION	6	A	71 - 86
7	X-RAY DIFFRACTION	7	A	87 - 108
8	X-RAY DIFFRACTION	8	A	109 - 134
9	X-RAY DIFFRACTION	9	A	135 - 192
10	X-RAY DIFFRACTION	10	A	193 - 229
11	X-RAY DIFFRACTION	11	A	230 - 247
12	X-RAY DIFFRACTION	12	A	248 - 264
13	X-RAY DIFFRACTION	13	B	19 - 38
14	X-RAY DIFFRACTION	14	B	39 - 62
15	X-RAY DIFFRACTION	15	B	63 - 79
16	X-RAY DIFFRACTION	16	B	80 - 101
17	X-RAY DIFFRACTION	17	B	102 - 112
18	X-RAY DIFFRACTION	18	B	113 - 137
19	X-RAY DIFFRACTION	19	B	138 - 166
20	X-RAY DIFFRACTION	20	B	167 - 191
21	X-RAY DIFFRACTION	21	B	192 - 211
22	X-RAY DIFFRACTION	22	B	212 - 244
23	X-RAY DIFFRACTION	23	B	245 - 256
24	X-RAY DIFFRACTION	24	B	257 - 264

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