PDB-2wkh: Crystal structure of the acyl-enzyme OXA-10 K70C-Ampicillin at pH 7

ID or keywords:

Entry

Database: PDB / ID: 2wkh

Title

Crystal structure of the acyl-enzyme OXA-10 K70C-Ampicillin at pH 7

Components

BETA-LACTAMASE OXA-10

Keywords

HYDROLASE / ANTIBIOTIC RESISTANCE / CLASS D BETA-LACTAMASE / PLASMID ENCODED

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: 1.791 Å

Authors

Vercheval, L. / Bauvois, C. / Kerff, F. / 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. / Sauvage, E. / Matagne, A. / Frere, J. / Charlier, P. / Galleni, M. / Kerff, F.

History

Deposition	Jun 11, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 25, 2010	Provider: repository / Type: Initial release
Revision 1.1	Apr 25, 2012	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2	Oct 1, 2014	Group: Non-polymer description / Structure summary
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

-
Download

PDBx/mmCIF format	2wkh.cif.gz	217.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2wkh.ent.gz	174.9 KB	Display	PDB format
PDBx/mmJSON format	2wkh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2wkh_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	2wkh_full_validation.pdf.gz	1.3 MB	Display
Data in XML	2wkh_validation.xml.gz	23.3 KB	Display
Data in CIF	2wkh_validation.cif.gz	33.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wk/2wkh ftp://data.pdbj.org/pub/pdb/validation_reports/wk/2wkh	HTTPS FTP

-
Related structure data

Related structure data	2wgvC 2wgwC 2wkiC 1k4fS 1e3u 1e4d 1ewz 1fof 1k4e 1k54 1k55 1k56 1k57 1k6r 1k6s 2wgi C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4wz5-1 1e4d-1 5mox-d 1h8y-d 2rl3-d 1k55-2 1e3u-1 2hp9-d 2wgi-d 3lce-1 1k56-2 4s2o-d 2hp6-d 1ewz-1 1ewz-2 2wgw-d 1k54-2 4wz5-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1)

Deposited unit

A: BETA-LACTAMASE OXA-10

B: BETA-LACTAMASE OXA-10

hetero molecules

56.6 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)	48.920, 97.090, 126.130
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: 27686.502 Da / Num. of mol.: 2 / Fragment: RESIDUES 20-266 / 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-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form) Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₂₁N₃O₅S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, LYS 70 TO CYS ENGINEERED RESIDUE IN CHAIN B, LYS 70 TO CYS

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.19 % / Description: NONE
Crystal grow	pH: 7 / Details: 0.7M AS, 0.1M HEPES PH 7

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.980026
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 13, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980026 Å / Relative weight: 1
Reflection	Resolution: 1.79→48.56 Å / Num. obs: 47137 / % possible obs: 82.1 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / B_iso Wilson estimate: 16.68 Å² / R_merge(I) obs: 0.16 / Net I/σ(I): 10.7
Reflection shell	Resolution: 1.79→1.89 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.9 / Mean I/σ(I) obs: 2.2 / % possible all: 59

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4F

1k4f

Resolution: 1.791→26.444 Å / SU ML: 0.31 / σ(F): 1.38 / Phase error: 26.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2592	2325	5 %
R_work	0.2002	-	-
obs	0.2032	46137	80.44 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 63.308 Å² / k_sol: 0.395 e/Å³

Displacement parameters

B_iso mean: 9.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.1915 Å²	0 Å²	0 Å²
2-	-	-4.4774 Å²	0 Å²
3-	-	-	-1.3619 Å²

Refinement step

Cycle: LAST / Resolution: 1.791→26.444 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3868	0	73	275	4216

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	4118
X-RAY DIFFRACTION	f_angle_d	1.446	5591
X-RAY DIFFRACTION	f_dihedral_angle_d	17.611	1507
X-RAY DIFFRACTION	f_chiral_restr	0.094	611
X-RAY DIFFRACTION	f_plane_restr	0.006	713

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7912-1.8277	0.4003	135	0.3402	2470	X-RAY DIFFRACTION	79
1.8277-1.8675	0.3723	103	0.3274	2133	X-RAY DIFFRACTION	88
1.9109-1.9587	0.4197	75	0.3125	1466	X-RAY DIFFRACTION	56
1.9587-2.0116	0.3317	153	0.2464	3033	X-RAY DIFFRACTION	96
2.0116-2.0708	0.2941	164	0.2284	3030	X-RAY DIFFRACTION	96
2.0708-2.1376	0.2967	182	0.2142	3096	X-RAY DIFFRACTION	98
2.1376-2.2139	0.293	84	0.2284	1771	X-RAY DIFFRACTION	57
2.2139-2.3025	0.3194	63	0.2619	1132	X-RAY DIFFRACTION	91
2.3025-2.4073	0.2777	160	0.1958	3183	X-RAY DIFFRACTION	100
2.4073-2.5341	0.2566	155	0.1837	3202	X-RAY DIFFRACTION	100
2.5341-2.6927	0.2499	179	0.183	3204	X-RAY DIFFRACTION	100
2.6927-2.9004	0.2428	189	0.1878	3192	X-RAY DIFFRACTION	100
2.9004-3.1918	0.2213	171	0.199	3224	X-RAY DIFFRACTION	100
3.1918-3.6526	0.2563	160	0.1922	3089	X-RAY DIFFRACTION	95
3.6526-4.598	0.2386	158	0.1765	3160	X-RAY DIFFRACTION	96
4.598-26.4465	0.1945	194	0.1496	3427	X-RAY DIFFRACTION	100

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	2.1091	-0.517	0.1194	0.7777	-0.4442	-0.3245	0.1714	0.3886	-0.0034	-0.2262	-0.2389	0.2394	0.4044	-0.3957	-0.0886	0.2016	-0.1314	-0.0189	0.372	-0.2273	0.1888	1.7257	-2.7754	46.5394
2	0.1446	0.0764	0.0055	0.2957	-0.1553	0.2482	-0.1047	0.0264	0.019	0.0304	0.0333	-0.0309	0.0475	0.0716	-0.0828	0.0746	0.0057	0.0168	0.1155	-0.0211	0.0583	13.5871	6.485	56.7859
3	0.0931	-0.3202	-0.0499	0.5849	-0.2161	0.2339	-0.2231	-0.2322	-0.2441	0.2306	0.22	0.3613	0.2288	-0.1588	0.0113	0.1861	0.0722	-0.0191	0.1713	-0.0097	0.0947	7.0092	19.0105	77.5919
4	0.248	-0.0821	-0.2228	0.4749	-0.048	0.0605	-0.0083	0.1161	0.1463	-0.083	0.0962	-0.1632	-0.0307	-0.0337	0.0769	0.1099	0.0263	-0.0159	0.0746	0.0225	0.062	13.2593	17.7344	70.0776
5	0.0896	-0.1063	-0.1695	-0.0401	-0.0237	0.5145	-0.07	0.0356	0.0067	0.0421	0.0121	0.0674	-0.0095	-0.038	-0.1221	0.0716	0.0207	0.0028	0.0706	0.0148	0.0748	18.6694	10.9745	60.9307
6	0.0326	0.0309	-0.2513	0.35	0.111	0.3599	-0.0099	-0.0058	-0.1379	-0.2111	-0.0906	-0.1448	0.3325	-0.1955	-0.0196	0.1763	0.0064	0.0011	0.1042	-0.019	0.0939	4.28	3.3022	63.8795
7	0.243	-0.0025	-0.4515	0.0781	0.1831	0.3314	0.0809	0.1761	0.021	-0.0976	-0.1861	-0.0568	0.2506	-0.0003	-0.0001	0.2172	-0.0113	0.0264	0.088	0.0069	0.1378	8.7519	0.2063	58.7724
8	0.2063	-0.0934	-0.2031	0.4517	0.2844	0.1241	0.0777	0.0691	-0.2747	-0.1855	-0.0825	0.4989	0.095	-0.312	-0.0141	0.1769	-0.0647	0.0277	0.1483	0.0009	0.1976	-1.26	1.8056	56.9026
9	0.0969	0.2625	0.1348	0.5423	-0.1734	0.0823	0.1492	0.0842	-0.1806	0.4386	-0.2489	0.0497	-0.054	-0.2436	0.0016	0.1067	-0.0068	0.0604	0.3809	0.0167	0.2021	-0.602	-6.2542	99.9147
10	0.5484	0.0524	0.0224	0.3116	0.2105	0.2699	0.1222	-0.1023	-0.3172	-0.1283	-0.1733	-0.0308	-0.0892	0.0047	0.0109	0.1614	0.0135	-0.0045	0.1184	0.0775	0.0968	14.6868	-7.7828	92.8941
11	0.4916	-0.6929	0.9859	0.2662	-0.5227	1.2734	-0.6984	-0.0947	-0.4852	-0.0545	-0.2509	-0.1439	-0.1274	0.1891	-0.1057	0.7147	0.209	0.2414	0.3108	-0.03	0.3813	23.1908	-18.5985	70.4566
12	-0.0008	-0.0214	-0.0341	-0.0086	0.0049	0.0395	0.0486	-0.0477	-0.047	-0.529	0.0773	-0.1255	-0.1351	-0.2607	-0	0.3412	-0.0747	-0.0134	0.179	-0.0236	0.2572	14.8964	-22.5638	73.4419
13	-0.0152	0.0525	0.0649	0.1139	0.0462	0.1944	0.0685	-0.1727	-0.3674	-0.1639	-0.0864	-0.1795	0.1899	0.031	-0.0001	0.2013	0.0149	0.0445	0.2027	0.0256	0.2716	22.4288	-18.2319	81.0611
14	0.5065	-0.1026	-0.2459	0.215	0.0746	0.5788	-0.0618	-0.0608	-0.1028	0.0655	-0.0308	-0.1376	-0.0091	0.0665	-0.0508	0.0662	0.0038	-0.008	0.0856	0.0452	0.1458	22.5573	-8.8594	89.8243
15	0.3148	0.0056	-0.1424	0.0413	0.2654	0.6739	-0.0351	-0.0482	0.0081	0.1583	-0.0615	-0.0878	-0.1694	-0.1702	-0.0599	0.0743	-0.0039	-0.0371	0.1146	0.0435	0.1317	7.269	-6.8951	86.8453
16	0.2982	0.2051	0.082	0.1141	0.0703	0.1885	0.0698	-0.0932	0.0036	-0.0032	0.0095	0.0859	0.1373	-0.3405	-0.0029	0.0739	-0.0113	-0.0487	0.1977	0.0307	0.1911	0.2093	-11.7142	90.2929

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND RESID 21:38
2	X-RAY DIFFRACTION	2	CHAIN A AND RESID 39:83
3	X-RAY DIFFRACTION	3	CHAIN A AND RESID 84:104
4	X-RAY DIFFRACTION	4	CHAIN A AND RESID 105:133
5	X-RAY DIFFRACTION	5	CHAIN A AND RESID 134:192
6	X-RAY DIFFRACTION	6	CHAIN A AND RESID 193:214
7	X-RAY DIFFRACTION	7	CHAIN A AND RESID 215:237
8	X-RAY DIFFRACTION	8	CHAIN A AND RESID 238:264
9	X-RAY DIFFRACTION	9	CHAIN B AND RESID 19:39
10	X-RAY DIFFRACTION	10	CHAIN B AND RESID 40:83
11	X-RAY DIFFRACTION	11	CHAIN B AND RESID 84:96
12	X-RAY DIFFRACTION	12	CHAIN B AND RESID 97:108
13	X-RAY DIFFRACTION	13	CHAIN B AND RESID 109:130
14	X-RAY DIFFRACTION	14	CHAIN B AND RESID 131:192
15	X-RAY DIFFRACTION	15	CHAIN B AND RESID 193:235
16	X-RAY DIFFRACTION	16	CHAIN B AND RESID 236:264

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi