PDB-3iof: Crystal structure of CphA N220G mutant with inhibitor 10a

ID or keywords:

Entry

Database: PDB / ID: 3iof

Title

Crystal structure of CphA N220G mutant with inhibitor 10a

Components

Beta-lactamase

Keywords

HYDROLASE / Antibiotic resistance / Metal-binding

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function

Biological species

Aeromonas hydrophila (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.44 Å

Authors

Delbruck, H. / Bebrone, C. / Hoffmann, K.M.V.

Citation

Journal: J.Med.Chem. / Year: 2010
Title: Mercaptophosphonate Compounds as Broad-Spectrum Inhibitors of the Metallo-beta-lactamases
Authors: Lassaux, P. / Hamel, M. / Gulea, M. / Delbruck, H. / Mercuri, P.S. / Horsfall, L. / Dehareng, D. / Kupper, M. / Frere, J.-M. / Hoffmann, K. / Galleni, M. / Bebrone, C.

History

Deposition	Aug 14, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 23, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jan 14, 2015	Group: Refinement description
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	3iof.cif.gz	119.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3iof.ent.gz	91.8 KB	Display	PDB format
PDBx/mmJSON format	3iof.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3iof_validation.pdf.gz	838.4 KB	Display	wwPDB validaton report
Full document	3iof_full_validation.pdf.gz	841.8 KB	Display
Data in XML	3iof_validation.xml.gz	15.3 KB	Display
Data in CIF	3iof_validation.cif.gz	22.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/io/3iof ftp://data.pdbj.org/pub/pdb/validation_reports/io/3iof	HTTPS FTP

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Related structure data

Related structure data	2wrsC 3iogC 1x8gS 1x8h 1x8i 3f9o 3fai S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5nbp-2 4y7u-d 2x1s-1 3iog-d 2x1u-2 5j64-d 5k9n-2 4eyf-2 4h0d-2 5j3p-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
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Beta-lactamase

hetero molecules

26.8 kDa, 1 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)	42.650, 100.660, 116.990
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-2- SO4
2	1	A-341- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Beta-lactamase Mass: 25163.768 Da / Num. of mol.: 1 / Mutation: N220G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: cphA / Plasmid: pET9a-CphA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P26918, beta-lactamase

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Non-polymers , 5 types, 305 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-IFS / bis(1-methylethyl) [2-(sulfanylmethyl)phenyl]phosphonate / Diisopropyl 2-(sulfanylmethyl)phenylphosphonate Mass: 288.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₃H₂₁O₃PS
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	THIS COORDINATES USE NON-SEQUENTIAL RESIDUE NUMBERING. THE NUMBERING RELATES TO PDB ENTRY 1X8G.

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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: 50.7 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2.4M (NH4)2SO4, 100mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 25, 2008 / Details: mirros
Radiation	Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.436→19.63 Å / Num. all: 46233 / Num. obs: 46231 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / B_iso Wilson estimate: 9.691 Å² / R_sym value: 0.041 / Net I/σ(I): 40.7
Reflection shell	Resolution: 1.436→1.51 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 16.3 / Num. unique all: 6547 / R_sym value: 0.112 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASER		phasing
REFMAC	5.5.0070	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8G

1x8g

Resolution: 1.44→19.59 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.969 / SU B: 1.292 / SU ML: 0.025 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.14145	2342	5.1 %	RANDOM
R_work	0.12284	-	-	-
all	0.12377	46231	-	-
obs	0.12377	46231	99.72 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 11.255 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.49 Å²	0 Å²	0 Å²
2-	-	0.5 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.44→19.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1776	0	87	290	2153

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	2045
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1429
X-RAY DIFFRACTION	r_angle_refined_deg	1.579	2.015	2777
X-RAY DIFFRACTION	r_angle_other_deg	1.504	3	3514
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.234	5	226
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.493	23.256	86
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.273	15	374
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.15	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	313
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	2072
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	387
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.583	1.5	1159
X-RAY DIFFRACTION	r_mcbond_other	0.194	1.5	457
X-RAY DIFFRACTION	r_mcangle_it	0.968	2	1923
X-RAY DIFFRACTION	r_scbond_it	1.591	3	886
X-RAY DIFFRACTION	r_scangle_it	2.284	4.5	854
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.436→1.473 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.154	176	-
R_work	0.122	3054	-
obs	-	3054	96.3 %

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	1.6463	2.2692	0.5615	7.2628	1.2008	1.5148	0.0096	-0.1365	-0.0104	0.3395	-0.0518	-0.0017	0.1122	-0.0476	0.0422	0.0665	0.0047	0.0041	0.046	0.0157	0.0317	8.513	30.539	58.726
2	1.0108	0.6914	0.1691	2.8117	0.7225	1.1097	0.0075	-0.1169	0.0157	0.1665	-0.0403	0.0455	0.0279	-0.0571	0.0328	0.0434	0.0035	0.004	0.0383	0.0041	0.0236	7.434	34.777	54.947
3	1.493	0.651	0.397	2.5309	-0.0859	0.7496	0.0122	0.0164	-0.1895	-0.0531	0.001	-0.1277	0.0999	0.0804	-0.0132	0.045	0.0123	0.0116	0.0251	0.0059	0.052	13.427	26.802	48.132
4	0.8912	-0.5361	0.4405	2.3672	-0.5868	1.1359	-0.0516	-0.075	0.0693	0.1779	-0.0038	-0.1694	-0.1071	0.0622	0.0554	0.0474	-0.0014	-0.0076	0.034	0.0047	0.0401	17.872	39.18	54.642
5	2.9975	1.1417	-0.5549	1.8961	1.0734	4.9977	-0.1013	-0.0741	0.0066	0.1363	0.0164	-0.1266	0.0475	0.118	0.0848	0.057	0.0171	-0.0111	0.0165	0.0145	0.0414	19.571	29.793	59.271
6	0.5848	-0.0445	-0.6288	1.5123	-2.5097	6.3075	0.0302	0.0334	-0.1077	-0.0611	-0.2069	-0.0706	0.3765	0.3761	0.1767	0.091	0.0277	0.0042	0.0457	0.0098	0.069	20.675	23.115	50.683
7	1.1882	-0.2205	0.4517	0.9471	-0.1229	1.1766	0.0119	0.0192	0.058	-0.0141	-0.0397	-0.069	-0.0039	0.0706	0.0278	0.0294	0.0008	0.0077	0.037	0.0082	0.0297	15.799	38.934	45.013
8	2.1721	-0.5033	1.9845	1.0104	-0.637	2.0605	0.0384	0.1215	-0.1176	-0.0958	-0.0187	-0.0269	0.0602	0.1537	-0.0197	0.0454	0.0099	0.0143	0.0619	0.0016	0.0402	16.62	34.986	35.849
9	1.7314	-0.289	0.067	3.3967	-0.3998	3.0545	-0.0007	0.1503	0.0758	-0.2944	-0.0223	-0.2106	-0.1615	0.1418	0.023	0.0609	-0.0031	0.0205	0.0405	0.0157	0.0318	15.282	45	33.55
10	4.1961	-0.8415	-1.5098	4.0208	2.8054	6.5234	0.0472	0.2202	0.1724	-0.2426	-0.1483	-0.0126	-0.5219	-0.076	0.1011	0.093	0.0077	-0.015	0.0207	0.0032	0.0419	11.898	51.817	43.12
11	2.6402	-0.9955	0.3124	4.9533	2.6579	5.0272	-0.0479	-0.123	0.2164	-0.1058	-0.0733	-0.0048	-0.4142	-0.027	0.1212	0.0965	-0.0038	-0.0115	0.0105	-0.0146	0.0531	13.462	53.887	51.465
12	0.8539	-0.1339	0.394	5.0924	2.5374	2.1999	-0.0044	0.1052	0.0478	-0.1447	-0.0498	-0.1304	-0.0997	0.1255	0.0542	0.0309	-0.0018	0.0268	0.0651	0.0191	0.0464	20.093	41.141	39.122
13	0.6042	0.0628	0.0909	2.8523	-1.2259	1.9313	0.0087	0.1409	-0.1862	-0.1375	-0.0761	-0.0805	0.1965	0.0197	0.0674	0.0697	0.0223	0.0151	0.0539	-0.0315	0.072	10.432	24.046	37.336
14	0.5719	-0.0681	0.0348	0.9464	-0.3911	0.9597	0.0014	0.0421	-0.0404	-0.0463	-0.0026	0.0358	0.0701	-0.0273	0.0012	0.0373	-0.0003	0.0017	0.0339	-0.0059	0.0291	2.322	31.857	39.724
15	1.3263	-0.0659	0.2008	1.3315	-0.6574	1.6548	0.0074	-0.0765	0.1406	0.1204	0.0392	0.0351	-0.1675	-0.1126	-0.0465	0.0504	0.0118	0.0013	0.0406	-0.0039	0.0368	-2.808	42.178	47.393
16	5.2406	1.2188	2.529	0.6947	1.5824	3.6365	-0.1611	0.0194	0.2949	-0.1267	0.0091	0.0669	-0.2887	-0.0368	0.1521	0.1033	0.0119	-0.0152	0.0543	0.0077	0.0698	-2.79	48.806	38.044
17	0.2341	-0.4752	0.3009	1.5389	0.2304	1.8936	0.016	-0.0104	-0.0454	-0.0649	-0.0088	0.0872	0.001	-0.1565	-0.0072	0.0298	-0.0111	-0.0037	0.067	0.005	0.0415	-7.143	35.569	35.65
18	0.2868	0.0101	0.236	1.6566	0.2346	1.5179	0.0041	-0.016	-0.01	0.0341	0.0116	0.0961	0.0774	-0.1487	-0.0156	0.0246	-0.0096	0.0061	0.0476	0.009	0.0407	-3.609	30.257	48.412
19	4.2412	-0.3937	-0.7492	3.913	-1.5615	3.0568	-0.0324	-0.0665	-0.0462	0.0808	0.096	0.1119	-0.0761	-0.2053	-0.0636	0.0099	0.0096	0.001	0.0769	0.008	0.0204	-10.145	37.649	45.41
20	9.3788	0.6516	-7.6329	5.1554	-1.3455	6.6376	0.4607	-0.0751	0.7011	0.3305	0.2287	0.3691	-0.7461	-0.2457	-0.6893	0.3806	0.2557	0.0538	0.2789	0.0846	0.1682	-11.499	49.154	39.564

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	41 - 48
2	X-RAY DIFFRACTION	2	A	49 - 71
3	X-RAY DIFFRACTION	3	A	72 - 86
4	X-RAY DIFFRACTION	4	A	87 - 96
5	X-RAY DIFFRACTION	5	A	97 - 102
6	X-RAY DIFFRACTION	6	A	103 - 111
7	X-RAY DIFFRACTION	7	A	112 - 131
8	X-RAY DIFFRACTION	8	A	133 - 141
9	X-RAY DIFFRACTION	9	A	142 - 149
10	X-RAY DIFFRACTION	10	A	150 - 157
11	X-RAY DIFFRACTION	11	A	158 - 166
12	X-RAY DIFFRACTION	12	A	167 - 175
13	X-RAY DIFFRACTION	13	A	176 - 188
14	X-RAY DIFFRACTION	14	A	189 - 218
15	X-RAY DIFFRACTION	15	A	219 - 233
16	X-RAY DIFFRACTION	16	A	234 - 240
17	X-RAY DIFFRACTION	17	A	241 - 252
18	X-RAY DIFFRACTION	18	A	253 - 291
19	X-RAY DIFFRACTION	19	A	292 - 301
20	X-RAY DIFFRACTION	20	A	302 - 307

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