PDB-4wd6: Crystal Structure of DIM-1 metallo-beta-lactamase

ID or keywords:

Entry

Database: PDB / ID: 4wd6

Title

Crystal Structure of DIM-1 metallo-beta-lactamase

Components

Metallo-beta-lactamase

Keywords

HYDROLASE / zinc metalloenzyme

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function

Biological species

Pseudomonas stutzeri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Booth, M.P.S. / Kosmopoulou, M. / Spencer, J.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of DIM-1 metallo-beta-lactamase
Authors: Booth, M.P.S. / Kosmopoulou, M. / Poirel, L. / Nordmann, P. / Spencer, J.

History

Deposition	Sep 7, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	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 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wd6.cif.gz	186 KB	Display	PDBx/mmCIF format
PDB format	pdb4wd6.ent.gz	150.5 KB	Display	PDB format
PDBx/mmJSON format	4wd6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4wd6_validation.pdf.gz	438.9 KB	Display	wwPDB validaton report
Full document	4wd6_full_validation.pdf.gz	444.5 KB	Display
Data in XML	4wd6_validation.xml.gz	19.5 KB	Display
Data in CIF	4wd6_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wd/4wd6 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/4wd6	HTTPS FTP

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Related structure data

Related structure data	1ddkS S: Starting model for refinement
Similar structure data	4gkx-6 6ck0-2 2jem-2 2ynu-1 3odd-d 3mnb-d 1tfo-d 6ck0-1 4jlb-1 2bga-1 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: Metallo-beta-lactamase

B: Metallo-beta-lactamase

hetero molecules

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

1

A: Metallo-beta-lactamase

hetero molecules

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

2

B: Metallo-beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	47.719, 47.856, 185.216
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Metallo-beta-lactamase Mass: 25738.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: patient isolate / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: blaDIM-1 / Plasmid: pXD-1 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: D5JGF6
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.91 Å³/Da / Density % sol: 35.68 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% polyethylene glycol (PEG) 550 monomethyl ether (MME), 10% PEG 20000, 50 mM HEPES / 50 mM MOPS pH 7.5 PH range: 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 21133 / % possible obs: 94.5 % / Redundancy: 7.1 % / R_merge(I) obs: 0.051 / Net I/σ(I): 32.5
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.251 / Mean I/σ(I) obs: 6.6 / % possible all: 68.4

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
HKL-2000		data reduction
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DDK

1ddk

Resolution: 2.2→42.55 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.918 / SU B: 14.586 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27397	1095	5.2 %	RANDOM
R_work	0.20654	-	-	-
obs	0.20989	20006	94.53 %	-

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: 51.26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.37 Å²	-0 Å²	0 Å²
2-	-	0.07 Å²	-0 Å²
3-	-	-	1.3 Å²

Refinement step

Cycle: 1 / Resolution: 2.2→42.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3392	0	4	126	3522

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	3462
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3271
X-RAY DIFFRACTION	r_angle_refined_deg	1.617	1.938	4698
X-RAY DIFFRACTION	r_angle_other_deg	0.84	3	7526
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.916	5	430
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.568	24.503	151
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.526	15	588
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.078	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	529
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3903
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	795
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	2.078	2.911	1729
X-RAY DIFFRACTION	r_mcbond_other	2.079	2.911	1728
X-RAY DIFFRACTION	r_mcangle_it	3.184	4.358	2156
X-RAY DIFFRACTION	r_mcangle_other	3.183	4.358	2157
X-RAY DIFFRACTION	r_scbond_it	1.843	3.068	1733
X-RAY DIFFRACTION	r_scbond_other	1.843	3.068	1733
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.862	4.534	2543
X-RAY DIFFRACTION	r_long_range_B_refined	7.064	24.261	4078
X-RAY DIFFRACTION	r_long_range_B_other	6.92	24.056	4037
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.203→2.26 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	65	-
R_work	0.239	1016	-
obs	-	-	65.91 %

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	5.6528	5.0901	0.0883	5.1032	0.2481	0.0564	0.3169	-0.8027	-0.6341	0.4085	-0.4593	-0.2734	0.0524	0.0532	0.1424	0.2141	0.0522	-0.0069	0.2604	0.1529	0.3202	-20.1625	-15.1553	-38.6868
2	5.0801	-5.2616	0.2033	5.8393	-0.833	7.0295	0.1061	0.05	0.54	-0.1809	0.0344	-0.3126	-0.0452	0.1573	-0.1405	0.2268	0.05	-0.0191	0.2497	-0.0018	0.2569	-4.5363	-4.6731	-46.6693
3	4.9444	2.2133	0.5314	4.2556	-0.4362	3.6316	0.0712	-0.1707	-0.0769	0.3015	-0.0629	0.214	0.0693	-0.2646	-0.0084	0.292	0.027	-0.0638	0.1477	-0.017	0.1262	-21.0311	-7.2641	-38.0207
4	1.1276	-0.1468	1.6752	2.7061	0.5983	3.0597	0.0647	0.0379	0.0576	-0.0775	-0.0269	-0.3862	0.0861	0.2983	-0.0378	0.2256	0.0251	-0.0177	0.1946	0.0116	0.159	-9.2472	-4.2587	-36.3473
5	5.3998	5.4114	2.5402	6.2039	3.4416	14.4253	0.0203	-0.1932	0.4933	0.3247	-0.1395	0.9167	-0.2889	-1.1679	0.1192	0.2817	0.0164	0.1033	0.243	0.0791	0.3652	-18.3622	-12.195	-30.9444
6	5.3483	-2.0751	0.7871	7.2562	1.7729	1.1823	-0.0722	-0.0435	-0.2838	0.0779	0.1607	-0.3143	0.3901	0.2009	-0.0884	0.4275	0.1072	0.0154	0.207	0.0313	0.2096	-5.9824	-14.5324	-33.8301
7	1.8957	-1.1289	0.7912	3.5509	-0.585	2.0379	0.0514	-0.1635	-0.1603	0.0937	0.0627	-0.0575	0.122	0.041	-0.1141	0.1754	-0.019	-0.0422	0.1694	0.0018	0.1226	-10.9177	-3.1999	-26.6341
8	4.3058	4.8656	-2.7565	6.1287	-3.3077	2.0003	0.1612	-0.4926	0.0145	0.4423	-0.1417	0.098	-0.0001	0.076	-0.0196	0.312	0.0422	0.0104	0.3885	0.0435	0.1294	-19.9073	3.8205	-18.2231
9	2.6052	2.372	-1.6175	7.074	-2.5512	4.1437	-0.0092	-0.1345	0.0154	0.262	-0.0176	-0.2405	-0.0206	0.0689	0.0267	0.2047	0.0062	-0.0628	0.2214	-0.0155	0.1835	-8.6522	5.4653	-23.1516
10	5.9066	-4.1499	2.3192	4.2845	-0.8591	1.5846	0.0955	0.4133	0.4552	-0.1263	-0.1517	-0.6974	0.078	0.4263	0.0563	0.2317	-0.0083	0.0019	0.2521	0.0307	0.2375	-4.8786	8.6851	-33.2886
11	1.7232	-0.3185	0.8791	3.6458	0.1778	5.3138	-0.0476	-0.0783	-0.0087	-0.1242	0.0206	-0.1875	-0.0403	0.241	0.0269	0.1775	-0.0194	-0.0263	0.097	0.0149	0.1338	-13.7801	7.6515	-38.3514
12	2.2569	-1.3113	-0.3745	1.2076	-1.1223	10.9662	-0.1635	-0.339	0.0103	0.3028	0.1218	0.1224	0.2027	-0.2004	0.0416	0.249	-0.0534	0.0269	0.2292	0.0119	0.2495	-28.5056	8.2631	-36.7567
13	10.7135	-2.5565	-8.816	0.9984	1.5148	10.8878	0.2987	-0.3611	1.1373	0.177	0.1259	-0.1183	-1.1152	0.0356	-0.4246	0.2573	0.0372	-0.0103	0.1972	-0.0459	0.3865	-23.3566	18.122	-36.5274
14	1.6347	-0.5552	0.294	5.4395	0.9076	1.9561	0.0197	0.2152	0.0639	-0.3898	-0.0319	-0.5357	-0.1844	0.4073	0.0121	0.1691	0.0102	-0.0082	0.1682	0.0251	0.142	-13.4994	9.8293	-44.607
15	12.5442	-2.1775	2.1768	9.8982	-1.1703	5.3296	-0.1934	-0.2351	0.1746	0.2596	0.2265	0.2411	-0.1574	-0.0629	-0.033	0.2052	-0.0083	-0.0412	0.1386	0.0203	0.1331	-25.0708	14.84	-44.302
16	2.0883	0.4771	-5.0082	0.6705	-1.9101	17.0566	-0.0999	0.4629	-0.0446	-0.1709	0.3583	0.5253	1.0457	-1.4581	-0.2585	0.2033	0.0003	-0.1105	0.3333	0.099	0.5597	-52.2778	-17.4824	-8.3128
17	17.7616	-0.7948	2.444	12.1125	-3.0725	1.4456	-0.3795	0.0828	0.2839	-0.2853	0.0076	-0.5655	-0.2365	0.3187	0.3719	0.3212	-0.0992	-0.1102	0.3175	0.0494	0.2521	-42.8511	-7.9923	-18.3338
18	4.708	-0.9493	-2.7243	1.3044	1.7274	10.5924	-0.025	-0.0671	-0.1564	-0.0145	-0.0325	0.387	0.2111	-0.1891	0.0575	0.1076	0.0153	-0.0402	0.1441	-0.0507	0.225	-45.8686	-17.771	-7.8456
19	5.7863	-0.1443	-1.5351	7.0461	-2.5691	1.6135	0.1041	0.4052	0.258	-0.6872	-0.1651	-0.192	0.2213	0.2215	0.061	0.1722	0.0275	-0.0493	0.3288	0.0112	0.2561	-41.1353	-16.8352	-17.8697
20	3.4731	1.0082	0.1281	3.156	-0.7909	8.9097	0.1191	0.531	0.0936	-0.5748	0.1383	0.1095	0.4834	0.0397	-0.2573	0.1837	0.025	-0.0365	0.2071	-0.0276	0.2295	-41.6602	-21.2981	-21.0952
21	10.3793	-4.0337	-3.8115	15.3283	4.444	2.3265	-0.3289	-0.9074	-1.1099	1.6524	0.2906	-0.0458	0.3401	0.2044	0.0382	0.2316	0.0103	0.0741	0.2739	0.1058	0.3349	-50.9119	-26.7737	-8.6089
22	2.2431	-1.9232	2.1727	2.0972	-1.0609	4.4481	0.1005	0.109	-0.2088	-0.2155	-0.2027	0.4488	0.1164	-0.3433	0.1022	0.2057	-0.0046	-0.0836	0.2142	-0.0399	0.2467	-51.0126	-21.3033	-22.1569
23	0.9911	-0.6597	0.8021	1.1736	0.1073	1.8538	0.1401	-0.0282	-0.2434	0.0168	-0.1308	0.0211	0.3804	-0.0493	-0.0094	0.2209	0.0059	-0.0325	0.2076	0.0088	0.2958	-38.8761	-31.855	-13.8229
24	0.95	-1.2334	0.8129	2.6991	-1.3614	0.9802	0.1285	-0.1126	-0.2693	0.1315	-0.0115	0.1721	-0.0689	-0.2523	-0.117	0.1716	0.0209	-0.0646	0.2473	-0.0374	0.2176	-37.8763	-37.2941	-14.4101
25	3.8812	0.6705	3.0486	0.3496	0.3787	3.936	-0.01	0.5907	-0.1928	-0.2856	0.1607	-0.0589	0.004	0.1694	-0.1507	0.3575	-0.0037	0.0213	0.2783	-0.0572	0.2452	-27.8095	-23.7546	-20.5939
26	3.8116	-0.3537	-0.0236	4.0674	1.7323	4.0055	-0.0002	0.1663	0.0432	-0.2064	0.0878	-0.0628	0.0177	0.1053	-0.0875	0.1012	-0.0228	-0.0119	0.1845	0.0009	0.2112	-30.8288	-17.4284	-9.554
27	2.3162	2.2428	0.1233	2.8216	0.0273	0.332	0.2361	0.0191	-0.6296	0.1315	-0.1333	-0.1918	0.397	-0.0355	-0.1028	0.4802	-0.0269	-0.1308	0.2596	-0.0317	0.4582	-27.7708	-25.2949	2.493
28	9.6131	1.9832	-0.9378	5.9797	1.8297	6.5102	0.0731	0.4792	0.072	-0.2832	-0.0007	-0.3949	-0.0157	0.8217	-0.0723	0.1379	0.0149	0.0314	0.2192	-0.0569	0.2208	-21.1372	-16.2407	-9.3056
29	6.3459	-0.0779	-0.0143	2.8629	0.3917	4.1265	-0.0615	0.2491	0.4646	-0.2215	0.0062	0.0822	-0.3658	-0.0421	0.0553	0.1656	0.0229	-0.0362	0.1709	-0.0069	0.1785	-33.1476	-10.1781	-8.4292
30	14.5121	-2.7033	3.7416	5.7233	5.1339	7.6838	0.1262	-0.4815	-0.0518	0.1875	0.1399	-0.3108	0.2152	0.0899	-0.2661	0.1147	-0.0464	-0.0025	0.1985	-0.0017	0.1926	-23.3784	-14.154	1.8551

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 9
2	X-RAY DIFFRACTION	2	A	10 - 15
3	X-RAY DIFFRACTION	3	A	16 - 28
4	X-RAY DIFFRACTION	4	A	29 - 50
5	X-RAY DIFFRACTION	5	A	51 - 55
6	X-RAY DIFFRACTION	6	A	56 - 66
7	X-RAY DIFFRACTION	7	A	67 - 102
8	X-RAY DIFFRACTION	8	A	103 - 110
9	X-RAY DIFFRACTION	9	A	111 - 124
10	X-RAY DIFFRACTION	10	A	125 - 135
11	X-RAY DIFFRACTION	11	A	136 - 163
12	X-RAY DIFFRACTION	12	A	164 - 176
13	X-RAY DIFFRACTION	13	A	177 - 181
14	X-RAY DIFFRACTION	14	A	182 - 208
15	X-RAY DIFFRACTION	15	A	209 - 220
16	X-RAY DIFFRACTION	16	B	4 - 9
17	X-RAY DIFFRACTION	17	B	10 - 14
18	X-RAY DIFFRACTION	18	B	15 - 32
19	X-RAY DIFFRACTION	19	B	33 - 40
20	X-RAY DIFFRACTION	20	B	41 - 50
21	X-RAY DIFFRACTION	21	B	51 - 55
22	X-RAY DIFFRACTION	22	B	56 - 70
23	X-RAY DIFFRACTION	23	B	71 - 108
24	X-RAY DIFFRACTION	24	B	109 - 117
25	X-RAY DIFFRACTION	25	B	118 - 135
26	X-RAY DIFFRACTION	26	B	136 - 166
27	X-RAY DIFFRACTION	27	B	167 - 177
28	X-RAY DIFFRACTION	28	B	178 - 192
29	X-RAY DIFFRACTION	29	B	193 - 209
30	X-RAY DIFFRACTION	30	B	210 - 220

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