PDB-4zej: Crystal Structure of DIM-1 Metallo-beta-Lactamase exposed to Ceft...

ID or keywords:

Entry

Database: PDB / ID: 4zej

Title

Crystal Structure of DIM-1 Metallo-beta-Lactamase exposed to Ceftazidime

Components

Metallo-beta-lactamase

Keywords

HYDROLASE / ZINC METALLOENZYME

Function / homology

Function and homology information

antibiotic catabolic process / periplasmic space / hydrolase activity / response to antibiotic / metal ion binding
Similarity search - Function

Biological species

Pseudomonas stutzeri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.79 Å

Authors

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

Funding support

United Kingdom, 1items

Citation

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

History

Deposition	Apr 20, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	May 27, 2015	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 / 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	4zej.cif.gz	189.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4zej.ent.gz	151.9 KB	Display	PDB format
PDBx/mmJSON format	4zej.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zej_validation.pdf.gz	435.7 KB	Display	wwPDB validaton report
Full document	4zej_full_validation.pdf.gz	436.8 KB	Display
Data in XML	4zej_validation.xml.gz	18.6 KB	Display
Data in CIF	4zej_validation.cif.gz	26.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ze/4zej ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4zej	HTTPS FTP

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Related structure data

Related structure data	1ddkS 4wd6 S: Starting model for refinement
Similar structure data	1eas-d 5abw-d 1uo6-d 1m9u-1 1e37-d 2bd7-d 1btu-d 3odd-d 1h9l-d 1e34-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: Metallo-beta-lactamase

B: Metallo-beta-lactamase

hetero molecules

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

1

A: Metallo-beta-lactamase

hetero molecules

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

2

B: Metallo-beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.397, 46.977, 183.758
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 / DIM-1 Mass: 25624.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source 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: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 192 / 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: 1.81 Å³/Da / Density % sol: 32.07 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 20% polyethylene glycol (PEG) 550 monomethyl ether (MME), 10% PEG 20 000, 50 mM HEPES, 50 mM MOPS

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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: 1.79→91.89 Å / Num. obs: 38481 / % possible obs: 99.6 % / Redundancy: 12.9 % / R_merge(I) obs: 0.088 / Net I/σ(I): 29.6
Reflection shell	Resolution: 1.79→1.86 Å / Redundancy: 7 % / R_merge(I) obs: 0.501 / Mean I/σ(I) obs: 2.5 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DDK

1ddk

Resolution: 1.79→91.88 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.959 / SU B: 4.516 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18907	1887	4.9 %	RANDOM
R_work	0.17235	-	-	-
obs	0.17316	36522	99.41 %	-

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: 35.641 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.61 Å²	0 Å²	-0 Å²
2-	-	0.75 Å²	-0 Å²
3-	-	-	-0.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.79→91.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3434	0	14	192	3640

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	3512
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	3312
X-RAY DIFFRACTION	r_angle_refined_deg	1.229	1.937	4766
X-RAY DIFFRACTION	r_angle_other_deg	0.895	3	7632
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.248	5	436
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.256	24.359	156
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.088	15	596
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.296	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	534
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3964
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	808
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	0.661	1.863	1750
X-RAY DIFFRACTION	r_mcbond_other	0.658	1.862	1749
X-RAY DIFFRACTION	r_mcangle_it	1.15	2.788	2184
X-RAY DIFFRACTION	r_mcangle_other	1.15	2.789	2185
X-RAY DIFFRACTION	r_scbond_it	0.576	1.948	1762
X-RAY DIFFRACTION	r_scbond_other	0.575	1.948	1762
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.011	2.889	2583
X-RAY DIFFRACTION	r_long_range_B_refined	4.816	15.254	3931
X-RAY DIFFRACTION	r_long_range_B_other	4.538	14.962	3877
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.794→1.84 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.228	108	-
R_work	0.217	2499	-
obs	-	-	93.31 %

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	5.5887	-1.3997	-0.353	3.0313	-0.0694	3.1668	0.117	0.0178	0.0645	0.0509	-0.1109	-0.0256	-0.2225	0.0704	-0.0062	0.1246	-0.056	-0.0032	0.0507	0.0004	0.1069	-17.102	7.773	39.669
2	2.0214	1.7374	-0.5704	3.8273	-0.4	2.3934	0.0811	0.0779	-0.0121	0.0231	-0.1252	-0.2131	-0.2661	0.4953	0.044	0.0595	-0.0443	0.0175	0.164	0.0494	0.0897	-7.521	8.016	33.592
3	3.6617	2.167	-0.2174	4.5719	-0.4584	2.2826	0.1004	0.3283	-0.0544	-0.1225	-0.126	-0.0944	0.0123	0.3357	0.0255	0.1109	0.0172	0.0111	0.1571	0.0503	0.07	-11.038	1.081	29.3
4	1.8616	1.0834	-0.7508	4.0641	-1.5367	2.5349	-0.0131	0.3237	0.0929	-0.4059	-0.037	-0.0913	0.0372	0.3639	0.0502	0.0845	0.0166	0.0164	0.1779	0.0372	0.027	-10.41	3.445	23.42
5	6.5384	-0.998	1.4534	11.299	-2.2673	6.6736	-0.1348	0.532	0.0692	-0.8246	0.233	0.3167	0.3306	-0.262	-0.0981	0.163	-0.0154	-0.0211	0.1447	0.0149	0.0533	-18.881	-3.526	18.516
6	1.7934	0.1402	0.7086	3.8856	-1.9625	4.9408	0.079	0.3104	-0.1882	-0.514	-0.3886	-0.653	0.6271	1.1204	0.3095	0.1863	0.1574	0.1113	0.3537	0.0411	0.2193	-3.917	-7.395	27.047
7	1.7504	0.3881	-0.3076	2.0375	-1.0899	2.541	0.0449	0.1394	-0.0637	-0.0846	-0.1175	-0.1236	0.263	0.3272	0.0726	0.1214	0.0581	-0.0109	0.0638	-0.0003	0.1142	-14.081	-9.252	37.261
8	1.9056	1.4205	0.0249	1.7554	-1.2605	4.8651	-0.1085	0.2172	-0.0254	-0.2839	0.1327	0.1424	0.3511	-0.2241	-0.0241	0.2246	0.0001	-0.0483	0.1051	-0.0397	0.1842	-24.968	-13.898	35.794
9	2.8271	-0.666	-0.4153	3.129	-0.2888	1.5128	0.0345	0.0231	-0.139	0.1637	-0.1895	-0.3098	0.1573	0.3176	0.155	0.1203	0.0433	-0.0183	0.0922	0.0284	0.1329	-12.074	-9.752	43.417
10	9.3869	5.643	3.0444	5.9417	0.6795	4.0658	-0.0986	-0.01	-0.368	-0.1701	0.1012	-0.0857	0.0543	0.0434	-0.0025	0.1412	0.032	0.0169	0.0176	0.0113	0.1285	-21.403	-13.784	45.486
11	4.8361	0.22	3.021	1.8874	0.2739	4.4367	-0.1424	-0.0556	0.1417	-0.0913	-0.0188	0.134	-0.1828	-0.2378	0.1613	0.0541	-0.0121	0.0233	0.1854	0.0651	0.0955	-44.344	-30.302	7.563
12	2.9013	1.2213	0.4469	1.2508	-0.0537	5.9347	0.1582	-0.4118	-0.0405	0.1299	-0.087	0.1231	-0.1876	0.1277	-0.0711	0.0538	-0.0139	0.0268	0.2306	0.072	0.0704	-39.757	-28.353	16.722
13	2.9171	1.7344	-1.169	5.0801	-1.7658	9.176	0.1195	0.0105	0.3444	-0.1469	-0.0066	0.4825	-0.6528	-0.7678	-0.113	0.0956	0.095	0.028	0.2638	0.04	0.1137	-48.896	-23.746	13.408
14	8.6035	4.3885	-7.0703	2.4113	-3.0672	7.7173	0.4478	-0.3441	0.2508	0.1764	-0.3089	0.1744	-0.6442	-0.0725	-0.1389	0.1573	0.0002	0.0415	0.2118	0.0196	0.1423	-40.686	-23.014	17.886
15	4.7127	0.4163	-1.5578	2.4497	0.4037	3.8736	0.3226	-0.3607	0.5664	0.3252	-0.1635	0.2742	-1.1091	-0.2459	-0.1591	0.4316	0.0428	0.0695	0.1568	-0.0028	0.1296	-37.475	-14.659	16.011
16	5.2187	-1.5495	0.282	5.0203	-0.7401	6.964	0.2419	-0.6886	0.5752	0.5217	-0.0978	-0.2766	-1.0426	0.1973	-0.1442	0.3939	-0.165	0.0455	0.2028	-0.056	0.1026	-30.577	-16.6	19.303
17	2.3482	0.603	-0.6664	1.951	-0.0441	3.1302	0.167	-0.0826	0.0777	0.0099	-0.1141	-0.0177	-0.3308	0.0877	-0.0528	0.0719	-0.0338	-0.0055	0.1757	0.0906	0.1058	-26.949	-27.253	8.072
18	4.5717	-0.5867	-1.5478	1.5038	-2.2317	7.3833	0.104	-0.3004	0.0854	-0.0304	-0.218	-0.1984	0.0992	0.6099	0.114	0.0653	-0.0611	-0.0198	0.2467	0.0908	0.1152	-18.239	-29.942	8.098
19	4.9522	-0.729	2.3139	1.9586	-0.0015	3.8444	0.1368	-0.1685	-0.3376	-0.0428	-0.0652	0.0043	0.2253	0.035	-0.0715	0.047	-0.0241	-0.0156	0.17	0.1219	0.099	-29.18	-37.171	10.166
20	4.6194	1.0277	-3.5988	6.4581	-1.9885	10.055	0.2582	-0.0373	0.0523	-0.2329	-0.2671	0.0237	0.0781	0.4962	0.009	0.0415	0.0188	-0.0087	0.2228	0.07	0.0765	-21.266	-32.904	-0.983

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 33
2	X-RAY DIFFRACTION	2	A	34 - 67
3	X-RAY DIFFRACTION	3	A	68 - 81
4	X-RAY DIFFRACTION	4	A	82 - 101
5	X-RAY DIFFRACTION	5	A	102 - 112
6	X-RAY DIFFRACTION	6	A	113 - 131
7	X-RAY DIFFRACTION	7	A	132 - 165
8	X-RAY DIFFRACTION	8	A	166 - 184
9	X-RAY DIFFRACTION	9	A	185 - 203
10	X-RAY DIFFRACTION	10	A	204 - 219
11	X-RAY DIFFRACTION	11	B	3 - 29
12	X-RAY DIFFRACTION	12	B	30 - 49
13	X-RAY DIFFRACTION	13	B	50 - 62
14	X-RAY DIFFRACTION	14	B	63 - 81
15	X-RAY DIFFRACTION	15	B	82 - 107
16	X-RAY DIFFRACTION	16	B	108 - 128
17	X-RAY DIFFRACTION	17	B	129 - 178
18	X-RAY DIFFRACTION	18	B	179 - 189
19	X-RAY DIFFRACTION	19	B	190 - 208
20	X-RAY DIFFRACTION	20	B	209 - 220

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