PDB-2wgi: Crystal structure of the acyl-enzyme OXA-10 W154A-benzylpenicilli...

ID or keywords:

Entry

Database: PDB / ID: 2wgi

Title

Crystal structure of the acyl-enzyme OXA-10 W154A-benzylpenicillin at pH 6

Components

BETA-LACTAMASE OXA-10

Keywords

HYDROLASE/ANTIBIOTIC / HYDROLASE-ANTIBIOTIC COMPLEX / HYDROLASE ANTIBIOTIC COMPLEX / LYSINE CARBOXYLATION / HYDROLASE / ACYL-ENZYME / ANTIBIOTIC RESISTANCE / CLASS D BETA-LACTAMASE

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 /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Vercheval, L. / Falzone, C. / Sauvage, E. / Herman, R. / Charlier, P. / Galleni, M. / Kerff, F.

Citation

Journal: Biochemistry / Year: 2009
Title: Critical Role of Tryptophan 154 for the Activity and Stability of Class D Beta-Lactamases.
Authors: Baurin, S. / Vercheval, L. / Bouillenne, F. / Falzone, C. / Brans, A. / Jacquamet, L. / Ferrer, J.L. / Sauvage, E. / Dehareng, D. / Frere, J.M. / Charlier, P. / Galleni, M. / Kerff, F.

History

Deposition	Apr 20, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 23, 2011	Group: Database references
Revision 1.3	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_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	2wgi.cif.gz	108.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2wgi.ent.gz	84.2 KB	Display	PDB format
PDBx/mmJSON format	2wgi.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2wgi_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	2wgi_full_validation.pdf.gz	1.1 MB	Display
Data in XML	2wgi_validation.xml.gz	18.7 KB	Display
Data in CIF	2wgi_validation.cif.gz	25.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wg/2wgi ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wgi	HTTPS FTP

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Related structure data

Related structure data	2hp5C 2hp6C 2hp9C 2hpbC 2rl3C 1k4fS 1e3u 1e4d 1ewz 1fof 1k4e 1k54 1k55 1k56 1k57 1k6r 1k6s S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1k55-2 1ewz-2 2wkh-d 6skq-2 3lce-1 1k56-2 1ewz-1 4wz5-2 1k54-1 6skq-1 4wz5-1 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 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)	48.800, 93.100, 127.700
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: 27597.408 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-PNM / OPEN FORM - PENICILLIN G Mass: 336.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₂₀N₂O₄S / Comment: antibiotic*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, TRP 154 TO ALA ENGINEERED RESIDUE IN CHAIN B, TRP 154 TO ALA
Nonpolymer details	BENZYLPENICILLIN (PNM): COVALENT BOND BETWEEN THE BENZYLPENICILLIN AND SER-67
Sequence details	N TERMINAL METHIONINE AND GLYCINE ARE ADDED BY MOLECULAR BIOLOGY CONSTRUCT

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 53.7 % / Description: NONE
Crystal grow	pH: 6 Details: 2.2 M AS, BUFFER BICINE 0.1 M PH 9 SOAKING 2.2 M AS, BUFFER MES 0.1 M PH 6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 2005 / Details: OSMIC MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.79→46.57 Å / Num. obs: 14053 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / B_iso Wilson estimate: 62.6 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 15.1
Reflection shell	Resolution: 2.85→3 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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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: 2.85→13.65 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.882 / SU B: 34.496 / SU ML: 0.306 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26227	703	5 %	RANDOM
R_work	0.19156	-	-	-
obs	0.19492	13300	99.83 %	-

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: 20.2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	0 Å²	0 Å²
2-	-	0.22 Å²	0 Å²
3-	-	-	-0.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→13.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3785	0	52	32	3869

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	3918
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.49	1.964	5297
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.233	5	478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.939	25.118	170
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.039	15	699
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.275	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	585
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2907
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	1517
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.292	0.2	2692
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.114	0.2	88
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	0.171	0.2	27
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.148	0.2	4
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	0.22	1.5	2466
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.401	2	3845
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.597	3	1688
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.154	4.5	1452
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: 2.85→2.921 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.368	60	-
R_work	0.306	924	-
obs	-	-	99.8 %

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	13.7908	0.4184	7.2862	8.1791	-5.8857	8.4161	0.2239	0.3569	-0.1487	0.2728	0.0649	1.222	-0.82	-0.7417	-0.2888	0.7407	0.1038	0.041	0.5351	-0.219	0.2931	1.957	6.781	78.133
2	0.8843	0.0757	-0.3016	3.5607	2.8161	7.3456	-0.015	-0.1303	0.0476	0.2102	-0.0396	-0.199	-0.3984	-0.1181	0.0546	0.1692	0.0558	-0.0205	0.0897	0.0529	0.1404	8.397	-5.452	69.153
3	6.6108	3.8913	1.9332	3.3257	-1.6255	9.9383	-0.4021	0.7337	0.2238	-0.2686	0.2498	0.5126	0.5776	-0.4915	0.1523	0.2956	-0.0317	-0.0216	0.0856	-0.0826	0.2131	2.998	-16.591	45.995
4	5.6553	-1.7794	1.8926	4.0251	-6.6045	11.0534	0.0827	-0.1544	-0.0419	0.0434	0.1604	0.1469	0.0437	-0.1163	-0.2431	0.1388	-0.0805	-0.0214	0.1756	-0.0198	0.2209	5.102	-14.181	51.128
5	1.4607	-3.113	-3.6885	20.868	11.2069	20.1188	0.1279	-0.2562	-0.2597	0.3298	-0.1199	-0.483	1.3222	0.0826	-0.008	0.1891	0.1485	0.0224	0.1252	0.1021	0.3044	16.329	-20.483	63.35
6	132.6368	-91.5211	266.4604	63.1775	-182.6066	594.0423	6.782	3.2541	0.1674	-8.5683	-8.5044	1.0137	28.6782	8.7808	1.7224	1.907	0.3082	-0.2198	0.8679	0.5218	1.1386	3.988	-20.941	66.319
7	2.7099	-0.0696	-0.1182	3.0866	-0.0819	3.4766	-0.0991	-0.1386	0.0724	0.0696	0.043	-0.1949	-0.2353	0.1671	0.0561	0.1609	-0.0024	-0.0247	0.1174	0.0128	0.1486	10.393	-2.817	62.475
8	8.9806	4.3824	0.689	7.7398	-0.4793	5.1902	-0.2911	0.1429	0.8453	-0.1526	0.2371	0.991	-0.4776	-0.5182	0.054	0.1914	0.1541	-0.0072	0.229	0.0004	0.2578	-2.731	2.507	67
9	11.4651	-10.5692	-7.4034	42.4423	10.5106	5.438	-0.1082	0.938	0.087	-0.4312	-0.4228	1.9622	0.0643	-0.9338	0.5309	0.1608	-0.0002	-0.0424	0.4279	0.0426	0.0511	3.238	7.422	22.777
10	1.2567	-0.0286	0.0168	3.1446	-0.6548	3.7494	0.0422	0.1481	0.0379	-0.2521	-0.1071	-0.1295	-0.0253	0.2067	0.0649	0.0553	-0.0251	0.0642	0.1016	0.0027	0.1289	17.442	8.087	33.339
11	2.0496	0.4227	-1.1627	16.8007	0.5609	16.9673	-0.0224	-0.372	0.1918	0.6567	0.3227	0.4082	-1.4521	0.0881	-0.3003	0.3426	-0.2096	0.0497	0.2112	-0.1425	0.2021	23.31	22.507	53.102
12	1.0336	1.0551	-1.6646	4.9005	0.2366	4.9177	0.047	-0.0258	0.0626	0.0982	-0.2299	-0.5429	-0.415	0.8424	0.1828	0.0312	-0.0924	-0.0808	0.2352	0.0326	0.3223	28.759	11.421	41.607
13	7.9349	2.0575	8.713	0.5335	2.2592	9.5673	-1.2619	-0.1217	0.8689	0.2912	-0.062	-1.9536	0.1017	0.5188	1.3239	1.1798	-0.0613	0.1996	0.7061	0.0346	1.1903	30.652	17.598	32.107
14	4.1661	-0.9945	2.1029	4.7991	-1.6998	6.5206	0.1056	-0.1057	-0.2371	-0.2642	-0.0363	-0.3602	0.2599	0.4619	-0.0693	0.1045	-0.0055	0.0845	0.1857	-0.0461	0.3172	22.204	2.139	34.569
15	2.2122	-1.9804	0.9346	2.7931	1.3168	4.9403	-0.027	-0.0664	0.0606	0.1245	-0.0795	-0.0531	-0.2617	-0.0755	0.1065	0.1232	-0.0161	0.0474	0.1703	-0.0239	0.1934	11.603	9.262	37.121
16	8.1132	6.6929	1.1409	20.0847	3.1109	10.6997	0.2064	-0.3639	0.5546	0.1143	-0.2476	1.364	-0.8585	-1.0534	0.0412	0.1612	0.2193	0.1265	0.1932	0.0607	0.2615	3.101	13.996	34.947

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 33
2	X-RAY DIFFRACTION	2	A	34 - 81
3	X-RAY DIFFRACTION	3	A	82 - 104
4	X-RAY DIFFRACTION	4	A	105 - 124
5	X-RAY DIFFRACTION	5	A	125 - 143
6	X-RAY DIFFRACTION	6	A	154 - 158
7	X-RAY DIFFRACTION	7	A	159 - 238
8	X-RAY DIFFRACTION	8	A	239 - 264
9	X-RAY DIFFRACTION	9	B	19 - 33
10	X-RAY DIFFRACTION	10	B	34 - 87
11	X-RAY DIFFRACTION	11	B	88 - 104
12	X-RAY DIFFRACTION	12	B	105 - 142
13	X-RAY DIFFRACTION	13	B	143 - 156
14	X-RAY DIFFRACTION	14	B	157 - 185
15	X-RAY DIFFRACTION	15	B	186 - 242
16	X-RAY DIFFRACTION	16	B	243 - 265

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