PDB-3sd9: Crystal structure of serratia fonticola SFH-I: Source of the nucl...

ID or keywords:

Entry

Database: PDB / ID: 3sd9

Title

Crystal structure of serratia fonticola SFH-I: Source of the nucleophile in the catalytic mechanism of mono-zinc metallo-beta-lactamases

Components

Beta-lactamase

Keywords

HYDROLASE /

METALLOENZYME /

ALPHA-BETA / METALLO-BETA-LACTAMASE

Function / homology

Function and homology information

antibiotic catabolic process /

beta-lactamase activity /

beta-lactamase / response to antibiotic / zinc ion binding
Similarity search - Function

Biological species

Serratia fonticola (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.83 Å

Authors

Fonseca, F. / Saavedra, M.J. / Correia, A. / Spencer, J.

Citation

Journal: To be Published / Year: 2011
Title: Crystal Structure of Serratia fonticola Sfh-I: Activation of the Nucleophile in Mono-Zinc Metallo-beta-Lactamases
Authors: Fonseca, F. / Bromley, E.H.C. / Saavedra, M.J. / Correia, A. / Spencer, J.

History

Deposition	Jun 8, 2011	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 13, 2011	Provider: repository / Type: Initial release
Revision 1.1	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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sd/3sd9 ftp://data.pdbj.org/pub/pdb/validation_reports/sd/3sd9	HTTPS FTP

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Related structure data

Related structure data	1x8gS 3q6v S: Starting model for refinement
Similar structure data	5ew0-1 5que-d 3q6v-2 3nok-1 1q0u-1 5quf-d 5ew0-2 5t5o-4 3f9o-d 1vk2-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

B: Beta-lactamase

hetero molecules

52.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase

hetero molecules

defined by author&software
26.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-lactamase

hetero molecules

defined by author&software
26.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	32.965, 86.412, 72.193
Angle α, β, γ (deg.)	90.00, 90.07, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase / Mass: 26294.844 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 3-234 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia fonticola (bacteria) / Strain: UTAD54 / Gene: blaSfh-I, sfhI / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RMI1, beta-lactamase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	NON-SEQUENTIAL RESIDUE NUMBERING IS USED IN THIS ENTRY. IT IS THE STANDARD NUMBERING SCHEME FOR ...NON-SEQUENTIAL RESIDUE NUMBERING IS USED IN THIS ENTRY. IT IS THE STANDARD NUMBERING SCHEME FOR METALLO-BETA-LACTAMASES.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.09 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% PEG 3350, 0.1M AMMONIUM NITRATE, 3% ISOPROPANOL, PH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9529 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2008 / Details: Mirrors
Radiation	Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9529 Å / Relative weight: 1
Reflection	Resolution: 1.83→72.2 Å / Num. all: 35354 / Num. obs: 33217 / % possible obs: 94 % / Redundancy: 2.5 % / R_merge(I) obs: 0.07 / Net I/σ(I): 12.8
Reflection shell	Resolution: 1.83→1.9 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 2 / Num. unique all: 3348 / % possible all: 94.3

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
AMoRE		phasing
REFMAC	5.5.0072	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1X8G

1x8g

Resolution: 1.83→72.19 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.941 / SU B: 7.228 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21311	1663	5 %	RANDOM
R_work	0.18332	-	-	-
obs	0.18484	31529	93 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 11.27 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.44 Å²	0 Å²	-0.76 Å²
2-	-	0.56 Å²	0 Å²
3-	-	-	0.87 Å²

Refinement step

Cycle: LAST / Resolution: 1.83→72.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3637	0	2	266	3905

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	3750
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.334	1.959	5102
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.014	5	465
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.775	25.205	171
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.707	15	640
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.005	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	569
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2846
X-RAY DIFFRACTION	r_gen_planes_other
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	0.735	1.5	2298
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.14	2	3730
X-RAY DIFFRACTION	r_scbond_it	1.892	3	1452
X-RAY DIFFRACTION	r_scangle_it	2.811	4.5	1371
X-RAY DIFFRACTION	r_rigid_bond_restr	1.115	3	3750
X-RAY DIFFRACTION	r_sphericity_free	4.18	3	268
X-RAY DIFFRACTION	r_sphericity_bonded	1.778	3	3662

LS refinement shell

Resolution: 1.83→1.878 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.276	115	-
R_work	0.225	2302	-
obs	-	-	92.15 %

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	4.0026	-1.1358	-1.0265	1.2107	-0.3634	6.4169	-0.1095	0.0654	-0.0804	-0.1781	0.1311	0.1219	0.1803	-0.4859	-0.0216	0.1826	-0.0172	-0.0402	0.1444	0.0033	0.1152	6.793	-4.646	-2.309
2	5.5535	2.0378	-4.909	2.0465	-2.6036	7.1867	-0.0924	0.1407	0.1738	-0.2979	0.1226	0.1012	0.1994	-0.1354	-0.0302	0.1327	0.0213	0.0298	0.0866	0.0131	0.0859	9.802	-2.928	-0.576
3	7.9044	-2.3917	0.0451	6.7036	-1.9919	0.6662	0.0361	0.31	-0.1492	-0.5506	0.1467	0.3716	0.2143	-0.1	-0.1828	0.2576	-0.0533	-0.1004	0.1419	0.0292	0.2134	-0.763	-7.175	9.597
4	0.9149	-0.1884	-0.2924	2.1878	0.0661	0.9858	0.0736	0.0892	0.0339	-0.1678	-0.0017	-0.113	0.0767	0.1228	-0.0718	0.0969	0.0147	0.012	0.1147	0.0014	0.0708	13.828	-5.662	4.693
5	0.9778	-0.4178	-0.4586	1.4101	0.4301	1.8203	0.0203	0.0574	-0.0683	-0.1068	-0.0161	-0.0311	0.1674	0.1056	-0.0042	0.1268	0.0172	0.0109	0.0884	0.0064	0.0874	14.249	-10.803	4.589
6	1.2381	-0.1904	0.3437	2.4847	0.0356	0.6966	0.0025	-0.07	0.1028	0.0957	0.0074	-0.1639	0.0263	0.0362	-0.0098	0.0959	0.0008	0.0049	0.1094	0.005	0.1016	16.529	-6.806	16.159
7	6.5658	0.413	2.4554	3.5738	0.7963	3.9745	0.0836	-0.3662	0.0265	0.2412	-0.1055	0.1163	0.0214	-0.1818	0.0219	0.1416	-0.019	0.0376	0.1054	0.0117	0.0648	4.761	-9.13	23.124
8	0.3484	-0.1999	0.1373	1.1315	0.1561	0.5277	0.0038	0.0417	0.0887	0.0456	0.005	-0.2624	-0.0863	0.117	-0.0087	0.1138	-0.0168	0.0133	0.1084	0.0149	0.139	20.952	2.752	13.033
9	1.436	-0.1433	0.651	1.3452	-0.1541	0.5765	-0.0295	0.0704	0.0961	-0.0649	-0.009	-0.058	-0.0247	-0.1247	0.0385	0.1335	-0.0081	0.0237	0.1111	0.015	0.1242	13.641	6.922	7.423
10	1.0968	-0.2209	-0.5412	4.422	-2.0984	1.3813	0.0898	0.2184	-0.1572	-0.1407	0.038	0.4396	0.0298	-0.1499	-0.1278	0.1536	-0.0129	0.0093	0.1123	-0.0025	0.1514	1.542	7.435	18.397
11	3.7542	-1.2132	2.0599	5.7087	1.3724	8.3975	0.068	-0.3381	0.0464	0.1906	-0.09	0.3092	-0.1273	-0.2542	0.0219	0.1167	-0.0029	0.02	0.0803	-0.026	0.0999	8.533	15.838	19.353
12	1.9908	2.1651	-3.7873	6.0499	-2.2206	8.5689	0.1398	-0.0909	0.0197	0.0107	-0.1211	-0.1564	-0.3255	0.2637	-0.0188	0.152	-0.0163	0.0022	0.1046	0.0197	0.139	16.626	19.238	7.419
13	3.1212	0.2754	-1.8583	2.2681	-0.207	3.8912	0.0135	0.0799	0.1272	-0.2886	0.0201	0.0908	0.015	0.1011	-0.0336	0.1157	0.0051	0	0.1011	0.0136	0.1163	9.731	8.642	2.576
14	2.3086	-0.6027	1.2611	1.9534	1.6489	2.8704	-0.1304	-0.0573	-0.0386	-0.1174	-0.0998	0.2534	-0.2302	-0.1395	0.2302	0.1207	0.0063	0.0033	0.1135	0.025	0.1813	2.863	12.541	6.293
15	10.6863	2.9117	3.3374	1.0586	1.1278	2.9046	0.0124	-0.2347	0.5787	0.0744	-0.1006	0.0933	0.0171	-0.6518	0.0882	0.2809	0.0801	0.0557	0.247	-0.0285	0.295	-2.971	18.375	18.686
16	3.4875	-0.7039	1.787	1.8142	0.9036	7.5891	-0.2481	0.0505	-0.189	-0.4916	0.2589	-0.2392	-0.314	0.4527	-0.0108	0.2365	-0.0269	0.1138	0.1482	-0.0136	0.1419	9.629	10.501	-38.203
17	3.827	1.1928	3.5625	1.8422	2.1958	5.0462	-0.0244	0.2591	-0.03	-0.1483	0.0894	-0.1362	-0.1516	0.3169	-0.065	0.1355	-0.0018	0.0529	0.1	-0.0022	0.0779	11.199	10.607	-32.354
18	1.3829	-0.2118	0.4606	1.7995	0.2956	1.4	0.0141	0.0887	-0.0559	-0.1593	0.0062	0.1407	-0.0781	-0.1308	-0.0203	0.1071	0.0105	0.0312	0.1003	-0.0074	0.0832	2.682	11.503	-31.391
19	1.2132	-0.4812	0.5521	1.654	-0.395	3.7483	-0.119	0.1182	0.0887	-0.1988	0.0022	0.0149	-0.2481	-0.0061	0.1168	0.1444	0.0243	0.0328	0.0784	-0.0029	0.0891	2.416	19.292	-34.733
20	1.5038	-0.6746	0.1709	3.539	-0.6799	0.9193	0.0231	-0.0264	-0.0248	-0.0115	-0.0121	0.1007	-0.0051	-0.0414	-0.011	0.09	0.0034	0.0392	0.0981	-0.0082	0.0745	1.137	13.487	-22.485
21	5.3236	2.437	0.6323	1.9461	0.3097	2.0247	0.0731	-0.3456	-0.203	0.3275	-0.1022	-0.0398	-0.0537	-0.0613	0.0291	0.1461	-0.0023	0.0481	0.0956	0.0193	0.0845	4.291	10.039	-11.644
22	9.3125	-1.7004	-3.9694	3.3785	-0.0302	2.0319	-0.0292	-0.487	-0.0676	0.3089	0.0024	-0.4109	-0.0907	0.4345	0.0268	0.1383	-0.0321	-0.0232	0.3468	-0.0702	0.1886	19.831	15.905	-15.358
23	1.0774	-0.0855	-0.1689	0.9195	-0.3677	0.8965	0.0522	-0.0164	-0.0779	0.0152	-0.0402	0.2193	0.0538	-0.1445	-0.0119	0.0901	0.0081	0.0531	0.0939	-0.0107	0.117	-3.145	8.924	-22.455
24	1.5605	-0.3982	0.2478	1.3039	-0.2607	1.6884	-0.0468	0.0293	-0.0635	0.0116	-0.0443	0.0446	0.0492	0.0089	0.0912	0.1125	-0.0169	0.0272	0.0848	-0.0149	0.1185	2.572	-1.643	-25.974
25	1.9304	0.8967	3.6754	8.9831	3.0849	7.2333	0.0182	-0.0161	0.017	0.0596	-0.0768	-0.0529	-0.0012	-0.0408	0.0585	0.1308	-0.0093	0.0072	0.1803	0.0074	0.1675	17.262	-1.813	-23.089
26	1.9253	3.932	0.4227	9.4489	-0.9558	2.4498	0.09	0.0422	-0.2076	0.1245	-0.0864	-0.4146	0.1235	0.2401	-0.0035	0.1651	-0.0082	0.0077	0.1487	0.0107	0.1603	12.27	-3.2	-12.782
27	2.1947	0.8276	2.2571	1.7482	1.2638	5.2018	0.0513	-0.0453	-0.2805	0.0358	-0.0564	0.0126	0.3363	-0.1672	0.0052	0.1296	-0.0081	0.0352	0.0837	0.0034	0.1031	2.542	-12.227	-24.417
28	3.7309	-1.5328	0.5972	1.2197	0.3451	5.1864	-0.0646	0.0688	-0.1143	-0.279	0.0637	-0.1239	-0.0619	-0.0911	0.0009	0.2003	-0.0274	0.0757	0.1185	-0.0198	0.1279	7.054	-2.866	-33.592
29	2.0906	-1.0868	-1.1554	3.6403	-0.783	1.2741	-0.0993	-0.0627	-0.0321	-0.1337	-0.0468	-0.2976	0.159	0.1031	0.1461	0.1066	0.0197	0.0473	0.1021	-0.0331	0.1499	13.294	-6.55	-30.235
30	10.5219	-2.8768	0.0105	2.2016	-3.6945	9.6332	-0.2292	-0.2494	-0.4482	0.1005	-0.1454	-0.0204	-0.0852	0.6055	0.3746	0.2567	0.0313	-0.075	0.1915	0.0062	0.3002	18.948	-12.033	-19.157

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	41 - 49
2	X-RAY DIFFRACTION	2	A	50 - 57
3	X-RAY DIFFRACTION	3	A	58 - 68
4	X-RAY DIFFRACTION	4	A	69 - 90
5	X-RAY DIFFRACTION	5	A	91 - 117
6	X-RAY DIFFRACTION	6	A	118 - 146
7	X-RAY DIFFRACTION	7	A	147 - 169
8	X-RAY DIFFRACTION	8	A	170 - 197
9	X-RAY DIFFRACTION	9	A	198 - 224
10	X-RAY DIFFRACTION	10	A	225 - 238
11	X-RAY DIFFRACTION	11	A	239 - 246
12	X-RAY DIFFRACTION	12	A	247 - 254
13	X-RAY DIFFRACTION	13	A	255 - 263
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