PDB-4tze: Structure of metallo-beta-lactamase

ID or keywords:

Entry

Database: PDB / ID: 4tze

Title

Structure of metallo-beta-lactamase

Components

Class B carbapenemase NDM-5

Keywords

HYDROLASE / Metallo-beta-lactamase / antibiotic resistance

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.574 Å

Authors

Ferguson, J.A. / Makena, A. / Brem, J. / McDonough, M.A. / Schofield, C.J.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: stucuture of metallo-beta-lactamase
Authors: Ferguson, J.A. / Makena, A. / Brem, J. / McDonough, M.A. / Schofield, C.J.

History

Deposition	Jul 10, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 29, 2015	Provider: repository / Type: Initial release
Revision 2.0	Sep 13, 2017	Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1	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 / 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	4tze.cif.gz	198.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4tze.ent.gz	157.3 KB	Display	PDB format
PDBx/mmJSON format	4tze.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4tze_validation.pdf.gz	438 KB	Display	wwPDB validaton report
Full document	4tze_full_validation.pdf.gz	441.1 KB	Display
Data in XML	4tze_validation.xml.gz	20.7 KB	Display
Data in CIF	4tze_validation.cif.gz	29.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tz/4tze ftp://data.pdbj.org/pub/pdb/validation_reports/tz/4tze	HTTPS FTP

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Related structure data

Related structure data	3spuS S: Starting model for refinement
Similar structure data	5zj7-d 2vvc-5 3cbc-3 2fbe-1 4u8t-1 5odl-d 5la9-1 6xbf-1 4zhh-1 4zhg-6 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: Class B carbapenemase NDM-5

B: Class B carbapenemase NDM-5

hetero molecules

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

1

A: Class B carbapenemase NDM-5

hetero molecules

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

2

B: Class B carbapenemase NDM-5

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.773, 59.216, 62.968
Angle α, β, γ (deg.)	90.00, 92.19, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Class B carbapenemase NDM-5 / NDM-5 metallo-beta-lactamase / New Delhi metallo beta lactamase 5 Mass: 24339.359 Da / Num. of mol.: 2 / Fragment: UNP residues 42-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaNDM-5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PlysS / References: UniProt: G3K399
#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.: 269 / 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: 2.06 Å³/Da / Density % sol: 40.29 % / Description: Cubic
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 10000, 0.1 M HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9785 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2013
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.57→35 Å / Num. all: 54576 / Num. obs: 54576 / % possible obs: 99.5 % / Redundancy: 0.5 % / R_merge(I) obs: 0.087 / Net I/av σ(I): 9.48 / Net I/σ(I): 9.48
Reflection shell	Resolution: 1.57→1.63 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.332 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-2000	v701c3	data reduction
HKL-2000	v701c3	data scaling
Coot	0.6.2	model building
PHASER	2.5.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SPU

3spu

Resolution: 1.574→34.07 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2343	1992	3.65 %	Random selection
R_work	0.1949	-	-	-
obs	0.1963	51507	99.45 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.574→34.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3362	0	4	269	3635

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3544
X-RAY DIFFRACTION	f_angle_d	1.006	4861
X-RAY DIFFRACTION	f_dihedral_angle_d	11.885	1214
X-RAY DIFFRACTION	f_chiral_restr	0.057	541
X-RAY DIFFRACTION	f_plane_restr	0.005	644

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 (%)
1.5738-1.6132	0.33	123	0.2808	3678	X-RAY DIFFRACTION	98
1.6132-1.6568	0.3161	148	0.2647	3759	X-RAY DIFFRACTION	100
1.6568-1.7055	0.3309	142	0.2557	3717	X-RAY DIFFRACTION	100
1.7055-1.7606	0.2915	140	0.2389	3770	X-RAY DIFFRACTION	100
1.7606-1.8235	0.2896	139	0.2329	3739	X-RAY DIFFRACTION	100
1.8235-1.8965	0.2894	150	0.2182	3747	X-RAY DIFFRACTION	100
1.8965-1.9828	0.2641	140	0.2068	3757	X-RAY DIFFRACTION	100
1.9828-2.0873	0.2196	155	0.1875	3737	X-RAY DIFFRACTION	100
2.0873-2.2181	0.2043	139	0.1804	3775	X-RAY DIFFRACTION	100
2.2181-2.3893	0.1902	145	0.177	3747	X-RAY DIFFRACTION	100
2.3893-2.6297	0.2405	143	0.1782	3782	X-RAY DIFFRACTION	100
2.6297-3.01	0.213	142	0.1858	3771	X-RAY DIFFRACTION	100
3.01-3.7915	0.2091	135	0.1788	3805	X-RAY DIFFRACTION	100
3.7915-34.078	0.2274	151	0.1848	3800	X-RAY DIFFRACTION	98

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	1.5554	-0.2636	-0.3963	0.5605	-0.133	0.1865	0.0914	-0.2371	0.2392	0.5137	0.125	-0.2604	0.1553	-0.0038	0.0766	0.278	0.0063	-0.0904	0.1641	-0.0424	0.141	10.8223	9.0895	83.1522
2	0.8891	0.0185	-0.1521	0.4596	-0.1118	0.0828	0.0726	-0.0708	0.2625	0.0683	0.0022	-0.0765	-0.1073	-0.2692	-0.0224	0.2611	0.05	-0.0028	0.1738	-0.0397	0.1531	3.3382	18.668	76.0331
3	0.7916	-0.285	0.2174	1.614	-0.4355	1.1731	0.11	-0.0966	-0.0047	0.028	-0.0488	0.018	0.0383	-0.0791	-0.0212	0.1466	0.0058	-0.0162	0.1064	-0.0187	0.1028	5.203	6.121	74.4932
4	1.9681	-0.8752	0.8959	2.649	-1.2754	2.5575	0.0198	0.0542	0.315	0.0879	-0.0637	-0.6251	-0.0808	0.1917	0.0374	0.1232	0.0093	-0.0001	0.1102	-0.0209	0.1702	14.6267	8.1001	72.5073
5	0.8776	-0.391	0.3583	1.0848	-0.0344	0.5138	0.0819	0.1032	0.0311	0.0915	-0.0911	0.0739	0.0614	0.0462	-0.0239	0.1205	0.0271	-0.0103	0.1086	-0.0107	0.1018	3.5192	5.5507	69.0366
6	0.7001	0.0415	0.1793	1.5885	0.3322	1.2319	0.0491	-0.028	0.0809	-0.3465	-0.1539	0.2908	0.082	-0.1186	0.1084	0.1548	0.0004	-0.0129	0.0984	-0.0381	0.1195	-2.9239	2.7036	62.7701
7	0.3117	-0.4101	0.1313	1.307	0.5408	1.2525	0.0593	-0.3819	0.1637	0.1893	-0.2571	0.5077	0.1998	-0.4698	0.0085	0.1067	-0.0358	0.0054	0.1948	-0.0809	0.2517	-7.6753	-0.2904	70.4965
8	1.2312	-0.4576	0.0758	1.4739	0.5626	0.8029	0.0543	-0.3911	0.2285	0.2944	-0.2144	0.6929	0.059	-0.5158	0.013	0.1791	-0.0364	0.0944	0.3612	-0.1508	0.3289	-11.1309	8.1625	78.446
9	0.9583	-0.1276	0.3026	0.019	-0.0224	0.3695	0.029	-0.4568	0.0717	0.2616	-0.1131	0.1211	0.2574	-0.3127	-0.1262	0.3863	-0.0944	0.1267	0.3472	-0.0701	0.1962	-5.0278	6.2451	84.5835
10	2.2422	-0.2604	-0.5156	3.2271	-0.0871	1.7047	0.174	0.0289	0.3237	0.0681	-0.0924	0.3985	0.0368	-0.0116	-0.0267	0.2205	-0.003	0.1028	0.3685	-0.0865	0.4565	-17.0385	12.131	83.8418
11	0.5366	0.1878	-0.0506	0.4879	0.0335	0.0139	0.184	-0.2608	0.0956	0.3463	-0.074	-0.1206	0.1864	-0.1499	0.3777	0.5963	-0.1116	-0.2423	0.1708	-0.0342	0.1361	35.7993	8.9884	114.6057
12	2.6153	0.5579	-1.2928	0.2216	0.0912	1.8746	0.2422	0.0108	0.3359	0.1533	0.1388	0.1162	-0.0619	-0.3259	0.2839	0.3437	-0.0404	-0.0644	0.137	-0.0301	0.0796	29.6891	16.9449	108.3219
13	0.654	-0.1947	0.3124	1.2361	0.1265	0.6887	0.1724	-0.0557	-0.0258	0.4455	-0.19	-0.1523	0.081	-0.0535	-0.0045	0.1605	-0.026	-0.0582	0.1048	0.0105	0.1335	32.4852	6.4162	103.6906
14	0.3884	0.6271	0.2461	1.7674	0.0375	0.6191	0.1373	-0.1447	0.1112	-0.036	-0.2149	0.3287	0.0294	-0.1017	0.0602	0.0902	-0.0146	0.0023	0.1282	-0.0365	0.1449	20.9031	2.0482	96.5646
15	1.4424	-0.4781	0.3605	1.6041	0.2596	1.0529	0.0313	-0.495	0.0941	0.6465	-0.0004	0.0785	0.0368	-0.2347	0.0105	0.3845	-0.091	0.1121	0.3229	-0.1068	0.1951	19.0289	5.7685	112.2026
16	1.1659	0.1719	0.6453	0.9912	0.3909	0.5508	-0.1646	-0.1067	0.4222	0.1919	-0.225	0.6176	0.0401	-0.2538	-0.2042	0.2589	-0.0245	0.1443	0.3166	-0.1481	0.4513	9.4465	11.4198	106.1806
17	0.0901	0.0073	0.1236	0.0872	-0.0394	0.6414	-0.0215	-0.191	-0.0232	0.3499	-0.0977	0.0841	0.0724	-0.2388	-0.1486	0.7124	-0.1784	0.2001	0.4325	-0.1582	0.0997	19.7316	7.7898	115.7235
18	1.5994	-0.9413	0.182	1.905	-0.941	1.3364	0.0494	0.007	0.2721	0.2666	-0.0814	0.5036	-0.0229	-0.2388	-0.1132	0.3883	-0.0422	0.2551	0.4424	-0.2112	0.5667	7.3246	13.6683	113.4494

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 41 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 70 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 94 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 95 through 108 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 109 through 128 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 129 through 170 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 171 through 194 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 195 through 239 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 240 through 255 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 256 through 270 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 42 through 57 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 58 through 70 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 71 through 128 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 129 through 194 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 195 through 215 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 216 through 240 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 241 through 255 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 256 through 270 )

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