PDB-2ynv: Cys221 oxidized, Mono zinc GIM-1 - GIM-1-Ox. Crystal structures o...

ID or keywords:

Entry

Database: PDB / ID: 2ynv

Title

Cys221 oxidized, Mono zinc GIM-1 - GIM-1-Ox. Crystal structures of Pseudomonas aeruginosa GIM-1: active site plasticity in metallo-beta- lactamases

Components

(GIM-1 PROTEIN) x 2

Keywords

HYDROLASE / ANTIBIOTIC RESISTANCE

Function / homology

Function and homology information

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

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Borra, P.S. / Samuelsen, O. / Spencer, J. / Lorentzen, M.S. / Leiros, H.-K.S.

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2013
Title: Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active-Site Plasticity in Metallo-Beta-Lactamases.
Authors: Borra, P.S. / Samuelsen, O. / Spencer, J. / Walsh, T.R. / Lorentzen, M.S. / Leiros, H.-K.S.

History

Deposition	Oct 18, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 24, 2013	Provider: repository / Type: Initial release
Revision 2.0	Jun 20, 2018	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations Category: atom_site / pdbx_struct_conn_angle ...atom_site / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type 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 / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2ynv.cif.gz	250.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2ynv.ent.gz	216 KB	Display	PDB format
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Validation report

Summary document	2ynv_validation.pdf.gz	441.8 KB	Display	wwPDB validaton report
Full document	2ynv_full_validation.pdf.gz	452.4 KB	Display
Data in XML	2ynv_validation.xml.gz	19.3 KB	Display
Data in CIF	2ynv_validation.cif.gz	26 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yn/2ynv ftp://data.pdbj.org/pub/pdb/validation_reports/yn/2ynv	HTTPS FTP

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Related structure data

Related structure data	2yntC 2ynuC 2ynwC C: citing same article (ref.)
Similar structure data	5acr-d 5acq-d 4c1d-d 6tgi-d 4brw-d 2ynu-d 6r5b-d 5oea-5 5act-d 5acs-d 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: GIM-1 PROTEIN

B: GIM-1 PROTEIN

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	38.648, 131.712, 40.721
Angle α, β, γ (deg.)	90.00, 94.78, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	GIM-1 PROTEIN / METALLO-BETA-LACTAMASE GIM-1 / METALLO-BETA-LACTAMASE Mass: 25667.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS PRARE / References: UniProt: Q704V1
#2: Protein	GIM-1 PROTEIN / METALLO-BETA-LACTAMASE GIM-1 / METALLO-BETA-LACTAMASE Mass: 25619.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS PRARE / References: UniProt: Q704V1
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	RESIDUES 1-18 IN THE GENE SEQUENCE ARE REMOVED AND A HIS TAG AND TEV CLEAVE SITE WAS INTRODUCED. A ...RESIDUES 1-18 IN THE GENE SEQUENCE ARE REMOVED AND A HIS TAG AND TEV CLEAVE SITE WAS INTRODUCED. A SERINE FROM THE TEV SITE IS THEN THE FIRST RESIDUE FOLLOWED BY GLN19 IN THE GENE.

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.01 Å³/Da / Density % sol: 38.92 % / Description: SOLVED USING ANOTHER GIM-1 STRUCTURE
Crystal grow	Details: 0.1M TRIS PH 7.1, 21% POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000 (PEG MME 2K), 4% GLYCEROL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97239 Å / Relative weight: 1
Reflection	Resolution: 2.05→41 Å / Num. obs: 24869 / % possible obs: 87.9 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / B_iso Wilson estimate: 39.37 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 10.5
Reflection shell	Resolution: 2.05→2.16 Å / Redundancy: 3 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→19.552 Å / SU ML: 0.29 / σ(F): 1.44 / Phase error: 27.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2472	1261	5.1 %
R_work	0.1967	-	-
obs	0.1994	24810	97.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.05→19.552 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3383	0	3	58	3444

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	3528
X-RAY DIFFRACTION	f_angle_d	1.645	4809
X-RAY DIFFRACTION	f_dihedral_angle_d	15.815	1274
X-RAY DIFFRACTION	f_chiral_restr	0.117	539
X-RAY DIFFRACTION	f_plane_restr	0.008	610

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 (%)
2.05-2.132	0.3113	136	0.2606	2653	X-RAY DIFFRACTION	99
2.132-2.2289	0.3155	161	0.2465	2602	X-RAY DIFFRACTION	99
2.2289-2.3462	0.3267	138	0.2435	2600	X-RAY DIFFRACTION	98
2.3462-2.493	0.2751	128	0.2264	2652	X-RAY DIFFRACTION	99
2.493-2.685	0.3108	120	0.215	2655	X-RAY DIFFRACTION	98
2.685-2.9544	0.268	135	0.2212	2613	X-RAY DIFFRACTION	98
2.9544-3.38	0.2407	122	0.2058	2627	X-RAY DIFFRACTION	97
3.38-4.2512	0.2291	158	0.1796	2562	X-RAY DIFFRACTION	96
4.2512-19.5527	0.2203	163	0.168	2585	X-RAY DIFFRACTION	96

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	1.2133	-0.498	-0.398	1.0769	-0.0506	1.6763	0.0315	0.1446	-0.1483	-0.1621	0.0091	-0.0316	0.1673	-0.0014	0.0626	0.0806	0.0219	0.0199	0.0748	-0.0627	0.0871	22.7059	-4.245	16.2779
2	3.2635	-0.1458	0.7268	0.2505	-0.2104	0.4893	0.0595	-0.0726	-0.1668	0.0655	-0.0574	-0.0477	0.0517	0.0259	-0.0433	0.053	-0.0121	-0.0241	0.1427	-0.0358	0.1239	23.7916	-3.6205	25.5462
3	3.2125	-0.6667	2.0385	1.8262	-0.0604	7.6585	0.0859	-0.075	-0.2458	-0.0314	-0.0099	0.1215	0.243	-0.1044	-0.0753	0.0818	-0.0147	-0.003	0.1649	0.1038	0.1902	15.3629	-8.4033	26.7899
4	2.4679	0.5485	0.9502	0.7761	0.2686	0.6962	0.0871	-0.241	-0.0802	0.0563	-0.0131	0.0583	0.0468	-0.1093	0.0157	0.0388	-0.005	0.0022	0.1624	0.0154	0.0449	6.675	-2.8784	29.0988
5	1.9189	-0.1446	0.6115	2.1066	-1.7156	2.1773	0.0871	-0.1413	-0.0633	-0.0007	0.0052	0.2148	-0.0968	-0.0991	-0.0736	0.0906	0.0117	0.0316	0.2038	-0.0348	0.1072	6.7146	-0.7254	30.4096
6	0.2693	0.1513	0.0648	0.3848	0.2169	0.2615	0.0597	-0.0043	0.0869	-0.027	-0.0033	-0.0091	-0.0733	-0.0033	0.0519	0.1236	0.0511	0.0328	0.0991	-0.0412	0.0833	10.9044	6.6134	17.9653
7	0.867	0.3095	-0.871	1.11	0.3094	1.6227	-0.1228	0.0573	-0.0782	-0.1006	0.0757	-0.0315	0.1975	-0.0939	0.0993	0.2137	0.1146	-0.0159	0.4095	-0.0711	0.1236	4.5973	-1.0924	6.7951
8	0.1667	0.0957	-0.1958	0.5653	0.0834	1.4309	0.0201	0.1748	0.0446	-0.138	0.0153	0.0367	-0.044	-0.2217	-0.0024	0.2007	0.1015	0.0348	0.3345	0.0365	0.0998	10.8166	3.9663	4.5994
9	1.3206	-0.0268	0.0279	1.7248	0.0259	2.0373	0.0885	-0.2229	0.2778	-0.0231	0.0136	0.0714	-0.1363	0.0812	-0.04	0.2903	-0.124	-0.1356	0.2259	0.0102	0.3768	3.512	-32.44	5.985
10	3.5272	-0.298	-0.617	0.3505	-0.0511	1.1344	0.107	-0.1276	0.4262	0.0328	0.0532	0.0777	-0.2459	-0.0002	-0.1723	0.233	-0.0846	-0.0458	0.2225	0.1178	0.3393	3.9031	-37.9064	11.2924
11	3.221	-1.2465	0.5181	2.3657	-0.7223	9.1806	-0.0151	-0.1695	0.0508	0.3175	0.0804	0.1459	-0.1538	-0.2377	-0.0583	0.155	0.025	0.0058	0.2588	0.1078	0.1324	8.2803	-41.0511	18.9748
12	5.6928	3.4873	1.9976	2.9297	2.5504	2.9195	0.1271	-0.1252	-0.2805	0.2594	-0.0127	-0.3789	0.185	0.2049	-0.1292	0.1705	-0.0314	-0.0548	0.1026	0.0425	0.1573	21.9368	-41.0771	13.0527
13	1.238	-0.955	-1.3946	0.8413	0.5827	4.9206	0.0059	-0.0603	0.1828	-0.1516	0.0663	-0.3191	-0.0847	0.0846	-0.0779	0.2045	-0.0176	-0.0892	0.0938	0.0578	0.3018	19.8951	-42.8197	14.3614
14	1.7237	0.2743	0.3681	1.9751	-0.2443	1.138	-0.0056	-0.0164	-0.0699	-0.1181	0.0133	-0.011	0.0894	-0.0489	-0.0065	0.3404	-0.1232	-0.0305	0.1606	0.0481	0.237	15.456	-41.436	-0.3033
15	1.5027	-0.5402	-1.1555	4.1099	0.0311	0.9262	-0.2153	-0.1557	0.4798	0.0341	0.0193	-0.1712	-0.4202	0.0791	0.2003	0.7686	-0.0232	-0.0975	0.4279	0.1208	0.5209	17.8537	-23.0746	-1.0488
16	3.5794	0.6104	-0.7673	4.9846	0.5832	4.0493	-0.0069	0.0695	0.0426	-0.2524	0.0526	-0.4614	-0.1682	0.2949	-0.0438	0.4377	-0.0969	0.1109	0.2348	0.1008	0.395	25.3344	-33.6927	-6.4994
17	0.8438	-0.7678	-0.3932	4.0176	1.0249	2.6964	-0.0048	0.0352	-0.0102	-0.2516	0.0073	0.1873	-0.0375	-0.0581	-0.0097	0.3405	-0.1537	-0.1407	0.2356	0.1217	0.2429	10.2493	-34.3688	-6.9558
18	4.9785	3.9752	-1.0099	6.1543	-0.2169	1.5635	0.0266	0.0618	0.1499	-0.0646	-0.0488	-0.4237	-0.339	0.408	-0.0056	0.6887	-0.1333	0.0992	0.4347	0.0985	0.3698	21.1839	-26.0979	-9.8524

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 40 THROUGH 88 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 89 THROUGH 118 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 119 THROUGH 131 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 133 THROUGH 149 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 150 THROUGH 175 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 179 THROUGH 222 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 223 THROUGH 252 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 253 THROUGH 295 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 40 THROUGH 89 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 90 THROUGH 122 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 123 THROUGH 136 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 137 THROUGH 148 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 149 THROUGH 175 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 179 THROUGH 222 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 223 THROUGH 238 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 239 THROUGH 252 )
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 253 THROUGH 279 )
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 280 THROUGH 295 )

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