PDB-2wki: Crystal structure of the OXA-10 K70C mutant at pH 7.0

ID or keywords:

Entry

Database: PDB / ID: 2wki

Title

Crystal structure of the OXA-10 K70C mutant at pH 7.0

Components

BETA-LACTAMASE OXA-10

Keywords

HYDROLASE / CLASS D / PLASMID ENCODED / ANTIBIOTIC RESISTANCE / 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 /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 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.L. / Sauvage, E. / Matagne, A. / Frere, J.M. / 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	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
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_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 1.4	Oct 9, 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	2wki.cif.gz	213.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2wki.ent.gz	173.3 KB	Display	PDB format
PDBx/mmJSON format	2wki.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wki_validation.pdf.gz	471.5 KB	Display	wwPDB validaton report
Full document	2wki_full_validation.pdf.gz	476.8 KB	Display
Data in XML	2wki_validation.xml.gz	23.3 KB	Display
Data in CIF	2wki_validation.cif.gz	33.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wk/2wki ftp://data.pdbj.org/pub/pdb/validation_reports/wk/2wki	HTTPS FTP

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Related structure data

Related structure data	2wgvC 2wgwC 2wkhC 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	3lce-2 5mmy-d 1e4d-1 1e3u-2 2hpb-d 1k55-1 2hp6-d 4wz5-1 1k54-2 5mox-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

56.8 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)	48.460, 96.300, 125.950
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 / 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.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 286 / 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
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: 2.44 Å³/Da / Density % sol: 49.26 % / Description: NONE
Crystal grow	pH: 7 / Details: 0.7M AS, PEG 10%, 0.1M HEPES PH7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.980026
Detector	Type: ADSC CCD / 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: 2.1→48.17 Å / Num. obs: 33372 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 8 % / B_iso Wilson estimate: 28.392 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 16.38
Reflection shell	Resolution: 2.1→2.2 Å / Redundancy: 7.9 % / R_merge(I) obs: 0.33 / Mean I/σ(I) obs: 5.5 / % possible all: 98.9

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4F

1k4f

Resolution: 2.1→48.17 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.933 / SU B: 7.078 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2022	1757	5 %	RANDOM
R_work	0.16464	-	-	-
obs	0.16651	33372	100 %	-

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: 16.116 Å²

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

Refinement step

Cycle: LAST / Resolution: 2.1→48.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3872	0	86	286	4244

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	4084
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.425	1.957	5508
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.586	5	504
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.508	25.169	178
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.327	15	723
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.03	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	598
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3012
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	1933
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	2852
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	255
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	0.186	0.2	27
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.114	0.2	8
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	0.832	1.5	2567
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.346	2	4001
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.313	3	1780
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.467	4.5	1504
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: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.237	125	-
R_work	0.16	2381	-
obs	-	-	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	22.3163	-7.2877	-14.3052	3.1166	4.1123	9.5945	-0.4974	0.6589	-0.7467	-0.0046	-0.2223	0.477	0.8914	-0.5903	0.7196	0.1557	-0.0644	-0.022	0.0746	-0.0832	-0.0169	4.4979	-4.7165	45.778
2	0.7001	0.1436	0.6625	1.3842	0.6064	1.9424	-0.0215	0.0437	0.0137	-0.0664	-0.0489	0.0657	0.0773	0.0319	0.0704	0.0461	-0.0134	0.0238	0.0504	0.004	0.048	11.4295	5.903	55.546
3	11.7829	-7.2728	2.889	5.1763	-1.2412	3.1621	-0.568	-0.3563	0.0219	0.4639	0.4006	0.0455	-0.292	-0.2039	0.1674	0.0768	0.0039	0.0019	0.0051	0.0225	0.0216	6.9081	18.7484	77.3897
4	3.2452	0.7085	-1.5329	3.4675	-1.6672	3.0049	-0.0511	0.0234	-0.1592	-0.052	0.0671	0.0196	0.192	-0.0307	-0.0159	0.0775	0.0075	-0.0123	0.0521	-0.0036	0.0451	8.8929	14.6363	72.3691
5	7.2251	-0.9108	-2.9052	5.1699	3.5231	4.9653	-0.0224	-0.0775	0.1774	-0.0595	0.1296	-0.0175	-0.271	0.1593	-0.1072	0.0679	-0.0175	-0.019	0.0535	0.0277	0.039	22.24	22.601	64.5479
6	0.9047	-0.1787	0.2114	1.7352	-0.2089	1.6274	-0.0397	0.0608	-0.0274	-0.0308	-0.0156	-0.0616	0.0446	0.0683	0.0554	0.0375	-0.0048	0.0104	0.0541	0.0016	0.0456	18.58	10.8996	60.4624
7	1.9664	-1.2616	0.6175	1.0542	-1.0593	1.9902	0.0218	-0.0331	-0.0529	-0.0573	-0.0987	0.1081	0.1755	-0.0411	0.0769	0.0886	-0.0218	0.0102	0.0511	-0.0058	0.061	6.1834	1.3611	66.259
8	1.5303	-1.9841	0.3905	4.1313	-0.4575	1.6093	-0.006	0.0127	-0.1521	-0.0614	0.037	0.219	0.1735	-0.1975	-0.031	0.045	-0.0499	0.0172	0.0766	0.0011	0.0461	3.0538	1.938	57.123
9	10.3964	7.6857	9.8188	13.0761	9.3956	9.8908	-0.1551	-0.3233	0.372	0.0477	-0.3618	0.5153	-0.1751	-0.941	0.5169	0.0685	-0.0402	0.0571	0.2125	0.0429	-0.0656	0.3339	-3.0613	100.3585
10	0.6653	0.0063	-0.3854	0.7898	-0.3591	1.8686	0.0024	-0.0994	-0.1644	0.0774	-0.0675	0.0002	-0.0041	-0.0127	0.0651	0.0317	-0.0283	-0.0304	0.0489	0.0347	0.0442	12.0226	-8.8388	93.2567
11	7.4131	8.9812	-0.1559	21.2945	-1.6022	5.2285	0.0408	0.1472	-0.7071	-0.9576	-0.0586	-0.6958	0.6835	0.2561	0.0178	0.1266	0.1492	-0.0107	-0.0258	0.003	0.0285	19.7039	-20.7242	71.5184
12	2.4354	-0.4792	-0.1582	6.2171	-2.5308	8.2385	0.1703	-0.0603	-0.4247	-0.3567	-0.2546	0.0533	0.3853	-0.2888	0.0842	0.0806	0.0103	-0.009	-0.0023	-0.0059	0.0935	15.327	-18.3672	72.5131
13	9.9154	0.9312	3.976	2.7483	-0.9056	4.3177	0.1753	0.0122	-0.3712	-0.1582	-0.0905	-0.2089	0.3046	-0.0355	-0.0848	0.0772	0.0413	0.046	0.0025	0.0555	0.0611	23.1617	-19.1681	81.491
14	1.3633	-0.3735	-0.2261	2.2917	-0.7917	2.5065	-0.0044	-0.087	-0.0195	0.0183	-0.1165	-0.2182	0.0084	0.1298	0.1209	0.0088	-0.0164	-0.0153	0.0395	0.038	0.0762	22.0364	-9.1142	89.4929
15	0.9973	-0.3772	0.4109	3.5026	-0.5456	1.8595	0.0379	0.0343	-0.1038	0.0685	-0.0205	0.1211	-0.0082	-0.1819	-0.0173	0.0243	-0.0041	-0.0054	0.0691	0.0255	0.057	7.0383	-7.4131	86.9255
16	1.8587	-1.3262	0.4114	8.5989	-0.8093	1.3359	0.0727	0.1169	-0.1194	-0.2562	-0.0289	0.3952	0.1591	-0.3145	-0.0438	0.0148	-0.0391	-0.0157	0.1243	0.0294	0.0442	-0.3008	-11.7958	89.7199

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 32
2	X-RAY DIFFRACTION	2	A	33 - 83
3	X-RAY DIFFRACTION	3	A	84 - 104
4	X-RAY DIFFRACTION	4	A	105 - 123
5	X-RAY DIFFRACTION	5	A	124 - 134
6	X-RAY DIFFRACTION	6	A	135 - 190
7	X-RAY DIFFRACTION	7	A	191 - 211
8	X-RAY DIFFRACTION	8	A	212 - 264
9	X-RAY DIFFRACTION	9	B	19 - 32
10	X-RAY DIFFRACTION	10	B	33 - 83
11	X-RAY DIFFRACTION	11	B	84 - 101
12	X-RAY DIFFRACTION	12	B	102 - 111
13	X-RAY DIFFRACTION	13	B	112 - 130
14	X-RAY DIFFRACTION	14	B	131 - 192
15	X-RAY DIFFRACTION	15	B	193 - 236
16	X-RAY DIFFRACTION	16	B	237 - 265

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