PDB-3v3r: Crystal Structure of GES-11

ID or keywords:

Entry

Database: PDB / ID: 3v3r

Title

Crystal Structure of GES-11

Components

Extended spectrum class A beta-lactamase GES-11

Keywords

HYDROLASE / Beta lactamase fold / Beta Lactams

Function / homology

Function and homology information

beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.898 Å

Authors

Delbruck, H. / Hoffmann, K.M.V. / Bebrone, C.

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2012
Title: Kinetic and crystallographic studies of extended-spectrum GES-11, GES-12, and GES-14 beta-lactamases.
Authors: Delbruck, H. / Bogaerts, P. / Kupper, M.B. / Rezende de Castro, R. / Bennink, S. / Glupczynski, Y. / Galleni, M. / Hoffmann, K.M. / Bebrone, C.

History

Deposition	Dec 14, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2013	Group: Database references
Revision 1.2	Sep 13, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3v3r.cif.gz	219.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3v3r.ent.gz	179.7 KB	Display	PDB format
PDBx/mmJSON format	3v3r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3v3r_validation.pdf.gz	444.4 KB	Display	wwPDB validaton report
Full document	3v3r_full_validation.pdf.gz	451.7 KB	Display
Data in XML	3v3r_validation.xml.gz	24.4 KB	Display
Data in CIF	3v3r_validation.cif.gz	35.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v3/3v3r ftp://data.pdbj.org/pub/pdb/validation_reports/v3/3v3r	HTTPS FTP

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Related structure data

Related structure data	3tsgC 2qpnS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ehn-d 4ehl-2 3v3s-2 4h8r-1 4euz-d 3gjt-2 4eha-1 3gjr-1 6kzq-d 6kmu-4 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	#164 - Aug 2013 Serotonin Receptor similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2) #29 - May 2002 Penicillin-binding Proteins similarity (1)

Deposited unit

A: Extended spectrum class A beta-lactamase GES-11

B: Extended spectrum class A beta-lactamase GES-11

hetero molecules

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

1

A: Extended spectrum class A beta-lactamase GES-11

hetero molecules

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

2

B: Extended spectrum class A beta-lactamase GES-11

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.680, 85.240, 85.120
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Extended spectrum class A beta-lactamase GES-11 / Extended-spectrum beta-lactamase / GES-11 Mass: 31206.465 Da / Num. of mol.: 2 / Fragment: BETA-LACTAMASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaGES-11, GES11 / Plasmid: PET28/GES11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C5HUY1, beta-lactamase
#2: Chemical	... ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 40.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M NA IODIDE, 30 % PEG 3350, 5 % GLYCEROL, pH none, VAPOR DIFFUSION, SITTING DROP, temperature 293K PH range: none

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å

Detector

Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 2, 2011 / Details: Mirror

Radiation

Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.926
1	1	-H, L, K	2	0.074

Reflection

Resolution: 1.88→20 Å / Num. all: 42480 / Num. obs: 40335 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / R_sym value: 0.114 / Net I/σ(I): 8.98

Reflection shell

Resolution: 1.88→1.92 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.523 / Mean I/σ(I) obs: 2.35 / % possible all: 87.2

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASER		phasing
REFMAC	5.6.0119	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QPN

2qpn

Resolution: 1.898→20 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.902 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23168	1988	5.1 %	RANDOM
R_work	0.19202	-	-	-
obs	0.19398	37055	94.51 %	-
all	-	39043	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 18.058 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.19 Å²	0 Å²	0 Å²
2-	-	-5.71 Å²	0 Å²
3-	-	-	13.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.898→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4041	0	24	264	4329

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	4252
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	2926
X-RAY DIFFRACTION	r_angle_refined_deg	1.377	1.963	5783
X-RAY DIFFRACTION	r_angle_other_deg	4.247	3.001	7136
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.97	5	570
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.201	23.548	186
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.066	15	751
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.342	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	662
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4815
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	876
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.898→1.947 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	129	-
R_work	0.26	2550	-
obs	-	-	89.9 %

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	4.4527	-0.1077	3.136	3.3726	3.4724	5.9517	0.0789	-0.181	-0.262	0.0516	0.0966	-0.0117	0.1145	-0.0132	-0.1755	0.102	-0.0344	0.0039	0.0655	0.0836	0.2865	55.804	-0.424	75.479
2	1.7758	-0.4471	-0.2388	1.7567	0.8723	0.4359	-0.007	0.0821	0.1047	0.0497	0.0601	-0.12	0.028	0.0387	-0.0532	0.1403	-0.0108	-0.0028	0.0494	0.034	0.1873	52.785	11.747	66.102
3	3.053	-1.0346	0.7365	16.7583	0.8009	0.2507	-0.1674	0.2143	0.092	0.0861	0.1575	-0.0567	-0.0557	0.0892	0.0098	0.1315	-0.0614	0.0274	0.1183	-0.0026	0.2608	38.652	22.549	57.166
4	1.8883	1.1138	0.0804	2.1208	0.6319	0.6998	-0.0373	0.1419	0.1101	0.033	0.043	0.0513	0.0446	-0.0946	-0.0058	0.1137	-0.018	-0.0107	0.0721	0.0189	0.1799	26.668	17.06	52.908
5	0.7819	-0.2825	0.2644	0.2945	0.2134	0.8743	-0.1055	0.1275	0.1108	-0.0502	-0.0243	0.0361	-0.0315	0.0588	0.1297	0.1462	-0.0175	-0.0288	0.0656	0.0263	0.2103	39.365	17.162	52.769
6	3.4638	1.2024	0.094	4.2173	0.7418	1.9147	0.0053	0.3131	-0.1404	-0.0374	-0.0087	0.0378	0.2603	0.1991	0.0034	0.1107	0.0115	-0.0078	0.0775	0.027	0.1584	47.037	7.865	51.76
7	0.1632	-0.3046	0.1738	1.0622	-0.3226	0.1954	-0.0496	-0.0065	0.021	-0.0006	0.029	0.034	-0.0832	0.0153	0.0205	0.139	-0.0423	0.0058	0.0811	0.007	0.2379	45.376	21.924	64.863
8	1.7453	-0.2863	0.3737	2.0569	-0.7135	0.4191	0.0343	-0.1782	-0.0673	0.1331	-0.0604	0.0284	-0.0188	-0.0448	0.0262	0.1335	-0.0124	0.0076	0.0845	0.0226	0.1551	37.382	12.662	74.245
9	1.0145	-0.4823	-0.2545	1.3093	-0.1214	0.525	0.0108	-0.0955	-0.0641	0.0946	0.082	-0.0001	0.0815	-0.0027	-0.0929	0.1024	-0.0106	0.0052	0.0551	0.0146	0.1875	45.296	8.772	69.106
10	4.9455	3.5563	2.5549	5.4259	1.2509	1.4464	0.0421	-0.0988	-0.1933	-0.0436	0.0204	-0.155	0.0201	-0.0645	-0.0625	0.1293	-0.0005	-0.0004	0.0451	0.0397	0.2698	42.499	-2.01	71.726
11	10.5533	-1.5439	-1.909	9.9888	-4.0398	2.2931	-0.295	-0.1772	0.2913	0.2518	0.4886	0.0693	-0.0101	-0.2835	-0.1936	0.2069	-0.085	-0.0554	0.4364	0.2129	0.2796	50.577	9.248	82.066
12	2.1542	1.1462	-0.2221	2.3221	-0.616	0.1864	-0.0889	0.1426	-0.0829	0.0108	0.1417	0.0432	-0.0087	-0.0605	-0.0528	0.1385	-0.0197	0.0055	0.0698	-0.0026	0.2295	-4.421	4.04	61.2
13	1.7433	2.2729	-0.7658	3.9134	-1.1754	0.3696	-0.0151	0.0386	0.1033	0.0077	0.0323	-0.0394	-0.0025	-0.0133	-0.0172	0.12	-0.0261	0.0053	0.0485	-0.0221	0.2303	5.793	14.732	72.775
14	9.5489	-2.9276	6.7896	4.9245	-1.9329	4.8334	-0.2565	-0.2353	0.2795	0.0601	0.058	0.1803	-0.1831	-0.1668	0.1985	0.098	-0.0148	0.051	0.0179	-0.0376	0.3975	17.884	31.997	72.557
15	1.5997	-1.3332	0.2799	2.8812	-0.6789	1.496	0.154	-0.2581	0.088	-0.0392	-0.2433	0.0627	0.2037	0.1385	0.0894	0.1447	-0.049	0.0043	0.2321	-0.0324	0.2095	25.011	15.176	81.053
16	1.6383	0.2822	-0.2578	0.6768	0.4662	0.4585	0.1036	-0.1823	0.0836	-0.0097	-0.0892	0.0315	-0.0376	-0.0069	-0.0145	0.1035	-0.0204	-0.0075	0.0917	-0.0159	0.2027	23.893	18.266	75.028
17	4.5136	-0.1469	0.897	1.6419	0.2215	0.5887	0.0661	-0.4288	0.2809	0.2131	-0.0969	0.0928	0.0032	-0.0314	0.0308	0.1234	-0.0347	0.0195	0.0766	-0.0504	0.229	7.107	19.649	79.666
18	1.1413	0.9212	-0.4696	1.1586	0.8599	4.6861	0.146	-0.1912	0.1453	0.0389	-0.1972	0.2527	0.0896	-0.0392	0.0513	0.2407	0.0017	-0.0932	0.0828	-0.0078	0.3287	0.288	13.738	73.502
19	3.5438	0.8244	1.2938	0.9367	1.8272	4.1858	0.0352	0.3049	0.5881	-0.1482	0.1119	-0.0599	0.1361	-0.0364	-0.1471	0.3855	-0.1789	0.029	0.1278	0.0337	0.3303	10.504	26.664	60.737
20	1.7226	2.6637	-0.4634	5.664	0.9356	2.0565	-0.1093	0.0754	-0.0599	-0.1397	0.1253	0.0593	0.0137	-0.0061	-0.016	0.0888	-0.0215	0.0257	0.0289	-0.0022	0.2661	14.971	11.216	60.921
21	1.4466	0.5258	0.3424	0.9142	0.7879	1.595	-0.0314	0.086	-0.0096	-0.0999	0.0468	-0.0534	-0.1375	-0.0021	-0.0154	0.0918	-0.001	0.0053	0.0449	-0.0029	0.2277	8.547	9.477	60.188
22	1.8009	-0.1105	0.379	1.2181	-1.2137	2.8694	0.015	0.05	-0.1357	-0.1085	-0.0094	-0.0227	0.3237	-0.0362	-0.0055	0.0837	-0.0405	-0.0088	0.0307	-0.0154	0.262	4.753	1.789	62.618

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	19 - 39
2	X-RAY DIFFRACTION	2	A	40 - 66
3	X-RAY DIFFRACTION	3	A	67 - 78
4	X-RAY DIFFRACTION	4	A	79 - 119
5	X-RAY DIFFRACTION	5	A	120 - 149
6	X-RAY DIFFRACTION	6	A	150 - 174
7	X-RAY DIFFRACTION	7	A	175 - 203
8	X-RAY DIFFRACTION	8	A	204 - 228
9	X-RAY DIFFRACTION	9	A	229 - 261
10	X-RAY DIFFRACTION	10	A	262 - 275
11	X-RAY DIFFRACTION	11	A	276 - 284
12	X-RAY DIFFRACTION	12	B	19 - 55
13	X-RAY DIFFRACTION	13	B	56 - 74
14	X-RAY DIFFRACTION	14	B	75 - 87
15	X-RAY DIFFRACTION	15	B	88 - 104
16	X-RAY DIFFRACTION	16	B	105 - 132
17	X-RAY DIFFRACTION	17	B	133 - 166
18	X-RAY DIFFRACTION	18	B	167 - 188
19	X-RAY DIFFRACTION	19	B	189 - 201
20	X-RAY DIFFRACTION	20	B	202 - 220
21	X-RAY DIFFRACTION	21	B	221 - 249
22	X-RAY DIFFRACTION	22	B	250 - 283

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