PDB-4u4l: Crystal structure of the metallo-beta-lactamase NDM-1 in complex ...

ID or keywords:

Entry

Database: PDB / ID: 4u4l

Title

Crystal structure of the metallo-beta-lactamase NDM-1 in complex with a bisthiazolidine inhibitor

Components

Beta-lactamase NDM-1

Keywords

HYDROLASE

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

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Kosmopoulou, M. / Hinchliffe, P. / Spencer, J.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the metallo-beta-lactamase NDM-1 in complex with a bisthiazolidine inhibitor
Authors: Kosmopoulou, M. / Hinchliffe, P. / Spencer, J.

History

Deposition	Jul 23, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 20, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4u4l.cif.gz	362.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4u4l.ent.gz	294.6 KB	Display	PDB format
PDBx/mmJSON format	4u4l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u4/4u4l ftp://data.pdbj.org/pub/pdb/validation_reports/u4/4u4l	HTTPS FTP

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Related structure data

Related structure data	3spuS S: Starting model for refinement
Similar structure data	6zyp-2 6zyq-2 4rm5-1 6c6i-2 5ypm-5 6twt-1 2c1f-d 6lhe-1 4rm5-4 6lj0-d 5ypi-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) 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

Related structure data

3spuS

S: Starting model for refinement

Similar structure data

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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 (4) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Beta-lactamase NDM-1

B: Beta-lactamase NDM-1

C: Beta-lactamase NDM-1

D: Beta-lactamase NDM-1

hetero molecules

106 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase NDM-1

hetero molecules

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

2

B: Beta-lactamase NDM-1

hetero molecules

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

3

C: Beta-lactamase NDM-1

hetero molecules

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

4

D: Beta-lactamase NDM-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.570, 69.023, 69.646
Angle α, β, γ (deg.)	87.39, 88.21, 76.75
Int Tables number	1
Space group name H-M	P1

#1: Protein	Beta-lactamase NDM-1 / NDM-1 / Metallo-beta-lactamase NDM-1 Mass: 26014.301 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: C7C422, beta-lactamase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-3C7 / (3R,5R,7aS)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid Mass: 237.363 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₇H₁₁NO₂S₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.09 Å³/Da / Density % sol: 41.19 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 25 %(w/v) PEG 2000 monomethyl ether

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 17, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 1.9→28.47 Å / Num. obs: 62122 / % possible obs: 93.5 % / Redundancy: 2.9 % / R_merge(I) obs: 0.045 / Net I/σ(I): 17.4
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.195 / Mean I/σ(I) obs: 5.4 / % possible all: 91

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SPU

3spu

Resolution: 1.9→27.881 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 17.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1816	3167	5.1 %
R_work	0.1541	-	-
obs	0.1555	62116	93.5 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→27.881 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6755	0	72	624	7451

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6982
X-RAY DIFFRACTION	f_angle_d	1.179	9509
X-RAY DIFFRACTION	f_dihedral_angle_d	13.313	2452
X-RAY DIFFRACTION	f_chiral_restr	0.054	1068
X-RAY DIFFRACTION	f_plane_restr	0.006	1250

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 (%)
1.9001-1.9284	0.2429	139	0.1872	2456	X-RAY DIFFRACTION	89
1.9284-1.9585	0.2166	122	0.1762	2452	X-RAY DIFFRACTION	91
1.9585-1.9906	0.1979	121	0.1695	2555	X-RAY DIFFRACTION	93
1.9906-2.0249	0.2171	157	0.1622	2590	X-RAY DIFFRACTION	94
2.0249-2.0618	0.2072	129	0.1597	2529	X-RAY DIFFRACTION	93
2.0618-2.1014	0.2155	143	0.1573	2557	X-RAY DIFFRACTION	92
2.1014-2.1443	0.2013	149	0.1544	2477	X-RAY DIFFRACTION	92
2.1443-2.1909	0.2063	160	0.1556	2499	X-RAY DIFFRACTION	92
2.1909-2.2418	0.2178	120	0.1536	2419	X-RAY DIFFRACTION	87
2.2418-2.2979	0.1611	124	0.1544	2524	X-RAY DIFFRACTION	92
2.2979-2.36	0.1973	143	0.1565	2596	X-RAY DIFFRACTION	96
2.36-2.4294	0.1774	135	0.1545	2664	X-RAY DIFFRACTION	96
2.4294-2.5077	0.1985	150	0.1529	2620	X-RAY DIFFRACTION	96
2.5077-2.5973	0.2061	130	0.1579	2624	X-RAY DIFFRACTION	96
2.5973-2.7012	0.1801	120	0.1574	2658	X-RAY DIFFRACTION	96
2.7012-2.824	0.1861	155	0.155	2589	X-RAY DIFFRACTION	95
2.824-2.9728	0.1704	138	0.1485	2570	X-RAY DIFFRACTION	94
2.9728-3.1588	0.1857	131	0.1639	2579	X-RAY DIFFRACTION	93
3.1588-3.4023	0.1837	125	0.145	2497	X-RAY DIFFRACTION	91
3.4023-3.7439	0.1616	147	0.1465	2649	X-RAY DIFFRACTION	97
3.7439-4.284	0.1407	143	0.1377	2660	X-RAY DIFFRACTION	96
4.284-5.391	0.1591	147	0.1452	2590	X-RAY DIFFRACTION	94
5.391-27.8844	0.1842	139	0.1689	2595	X-RAY DIFFRACTION	95

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	4.7696	-0.2225	-3.5053	3.652	1.7715	8.0077	0.177	-0.705	-0.2505	0.3495	0.2481	-0.3335	0.2668	0.8683	-0.2698	0.2167	0.0345	-0.0336	0.1723	0.0472	0.1805	22.0619	-19.588	-15.376
2	6.6085	0.8968	-0.8349	4.7292	0.024	4.851	0.0181	0.0255	0.0354	-0.1189	0.0232	-0.5491	0.038	0.5859	0.0444	0.1061	0.0224	0.0238	0.1461	0.0018	0.143	25.0684	-11.9981	-20.3243
3	2.4853	-0.515	0.799	2.8676	0.3753	1.2987	0.0498	0.0313	-0.1847	-0.1371	-0.0262	0.0667	0.1003	0.0382	-0.0162	0.1037	-0.019	0.0174	0.0907	0.0108	0.0905	15.3851	-13.5387	-25.6961
4	1.3534	-1.226	-1.7711	2.7268	1.4042	4.4321	0.0703	0.0211	-0.0353	-0.1789	-0.0632	0.0112	-0.0821	-0.0707	-0.0022	0.082	-0.0118	-0.0317	0.0759	0.0149	0.0628	9.2486	1.3263	-28.5298
5	2.2908	-0.1577	0.6926	2.3673	-0.3205	2.5127	-0.0587	-0.1236	-0.0746	0.157	0.0903	0.0657	0.0895	-0.0975	-0.0329	0.1116	-0.0026	0.0198	0.1118	0.0022	0.0496	10.1618	-1.7715	-17.1667
6	1.2315	-0.4218	0.6615	3.0257	-0.6025	1.9406	-0.1511	-0.0486	0.1156	0.178	0.1174	-0.2018	-0.0685	0.0367	0.0425	0.1577	-0.0012	-0.0326	0.1518	-0.0338	0.0809	18.7606	2.7596	-11.4172
7	3.2925	1.7031	-2.0011	4.2875	-2.5197	5.3443	-0.0431	-0.1228	0.2561	0.5765	-0.0763	-0.3408	-0.6542	0.2299	0.1153	0.2767	0.0384	-0.0838	0.1784	-0.0306	0.1422	21.25	8.0405	-6.6285
8	5.8041	1.0211	-1.2155	3.8736	0.1541	4.7325	0.1273	-0.2828	0.4937	-0.0031	-0.1781	-0.0886	-0.2828	0.1526	0.0366	0.137	0.0046	-0.01	0.118	0.0541	0.1335	13.3338	-17.8712	6.5581
9	3.9475	-0.2083	1.0445	3.8355	0.0715	6.7131	0.0117	-0.2697	0.1943	0.3159	0.0313	-0.1685	-0.1446	0.2146	0.011	0.0673	0.0066	0.001	0.0921	-0.0078	0.0977	14.133	-25.8479	12.1006
10	2.2762	-0.6917	0.4124	2.6931	-0.2872	4.2092	0.0525	0.119	0.0965	-0.0886	-0.0616	0.251	-0.2033	-0.0872	-0.0135	0.0645	0.0062	-0.0136	0.1081	0.0134	0.082	4.5572	-27.0418	6.147
11	6.387	-1.8038	3.5212	1.9717	-0.6084	3.4005	-0.0217	-0.1643	-0.3859	0.2709	0.1661	0.4753	0.0144	-0.1226	-0.1074	0.1084	-0.0155	0.0279	0.1154	0.0348	0.1849	6.26	-35.511	12.8961
12	1.7904	-0.5438	-1.7609	3.7796	1.587	2.0294	-0.076	-0.1654	-0.3201	0.1246	0.1001	0.169	0.2134	0.0508	-0.0192	0.0526	-0.008	0.0018	0.1059	0.0248	0.1908	8.4105	-44.8191	12.914
13	4.6944	-1.2515	-3.1138	2.2123	0.768	5.0004	0.1002	0.2679	-0.5184	-0.1081	-0.0032	0.2546	0.2446	-0.0103	-0.0552	0.1602	0.0131	-0.0898	0.1455	-0.043	0.1964	10.7086	-45.9197	4.724
14	1.9427	-0.7356	0.4445	2.2433	-0.2087	1.1116	0.0659	0.1768	0.1188	-0.1691	-0.1181	-0.246	-0.0459	0.1108	0.0567	0.0927	-0.0023	0.0343	0.1472	0.0133	0.1044	24.2678	-37.4888	6.4718
15	7.3797	-0.105	-5.2525	0.7663	1.2853	5.6849	-0.1419	-0.4348	-0.4835	0.6535	0.0094	-0.1279	0.5855	0.3723	0.1768	0.2286	0.025	0.0291	0.1352	0.0864	0.3395	40.7069	-15.1179	17.4553
16	2.116	-0.5238	0.297	2.9625	0.5667	3.3374	0.052	0.0332	-0.1795	-0.0678	-0.0124	-0.1061	0.1279	0.049	-0.0309	0.0769	0.0082	-0.0032	0.0728	0.0024	0.1337	38.1877	-9.3165	10.6559
17	1.8482	-0.469	0.0605	4.4063	0.6193	1.4667	0.0741	0.0858	-0.0519	-0.2966	-0.1411	-0.2527	-0.0264	0.0678	0.0417	0.1083	-0.0028	0.024	0.0994	0.0038	0.0916	39.609	3.1941	5.6137
18	1.9521	-0.8996	-2.0654	1.7347	0.8097	4.0153	0.1005	0.2581	0.0985	-0.1553	-0.1048	-0.1166	-0.174	-0.2481	-0.0086	0.1664	0.0066	-0.0244	0.0461	0.0143	0.1196	32.731	8.6213	6.1389
19	1.3931	0.1612	0.7103	2.6494	0.303	2.5899	0.0618	-0.009	-0.0772	-0.0381	-0.0287	-0.0089	0.096	-0.0596	-0.0288	0.0619	0.009	0.0156	0.0968	0.001	0.0558	29.382	3.1512	15.0723
20	3.4093	0.9891	0.5871	2.9479	-0.7718	2.9596	-0.0273	-0.0821	0.1527	0.179	-0.0063	-0.1778	-0.1053	0.1389	0.053	0.1067	0.016	0.0068	0.1076	-0.0242	0.0541	35.4476	11.3291	25.1764
21	3.8936	-3.8573	-0.5865	3.9975	-0.2681	4.6611	-0.2046	-0.2561	-0.2303	0.3554	0.2122	0.0228	0.0255	0.1635	-0.0121	0.1378	-0.0248	0.009	0.088	-0.0039	0.0771	30.981	-2.1323	24.711
22	7.1896	4.6741	1.5083	4.5785	1.9219	6.1766	-0.0298	-0.3792	0.2224	0.2087	-0.0639	-0.0397	-0.3356	0.0389	0.0737	0.1583	0.0236	0.0025	0.152	0.0027	0.0883	33.3102	10.0188	31.2812
23	5.1807	0.2066	2.706	4.6853	0.9006	6.2957	0.0951	0.0206	0.4222	-0.2338	-0.0769	-0.3103	-0.3499	0.0902	-0.0051	0.1471	0.0182	0.0451	0.0904	0.0074	0.1654	34.6533	-29.7073	-32.7075
24	1.0888	-0.7288	-0.0954	2.16	0.2045	0.9876	-0.0499	-0.0388	0.137	0.0449	0.0542	-0.0715	-0.1072	-0.0192	0.0028	0.0957	-0.0042	-0.0107	0.0952	-0.0074	0.0906	32.7072	-43.5469	-28.2585
25	4.0292	4.0017	-3.9619	5.5875	-6.3078	7.5181	0.2311	-0.5435	0.5846	0.4096	-0.1744	-0.2344	-0.5698	0.4372	-0.0493	0.1966	-0.0221	-0.021	0.2895	-0.0722	0.3382	53.8172	-45.4057	-28.3923
26	3.4646	0.3575	0.4377	3.727	0.345	3.5222	0.0769	0.1215	0.3905	-0.1425	-0.0749	-0.3876	-0.1283	0.1757	0.0019	0.1324	0.0047	0.0725	0.1398	0.0314	0.1839	48.8542	-44.3811	-38.2137

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 39 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 72 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 137 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 138 through 170 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 171 through 212 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 213 through 255 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 256 through 270 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 40 through 57 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 58 through 82 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 83 through 118 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 119 through 137 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 138 through 152 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 153 through 170 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 171 through 270 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 43 through 55 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 56 through 118 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 119 through 149 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 150 through 170 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 171 through 212 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 213 through 239 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 240 through 255 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 256 through 270 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 41 through 82 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 83 through 212 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 213 through 228 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 229 through 270 )

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About Yorodumi

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Yorodumi