PDB-3tsg: Crystal structure of GES-14

ID or keywords:

Entry

Database: PDB / ID: 3tsg

Title

Crystal structure of GES-14

Components

Extended-spectrum beta-lactamase GES-14

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: 1.9 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	Sep 13, 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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PDBx/mmCIF format	3tsg.cif.gz	227.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3tsg.ent.gz	185.2 KB	Display	PDB format
PDBx/mmJSON format	3tsg.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3tsg_validation.pdf.gz	458.6 KB	Display	wwPDB validaton report
Full document	3tsg_full_validation.pdf.gz	467 KB	Display
Data in XML	3tsg_validation.xml.gz	26.6 KB	Display
Data in CIF	3tsg_validation.cif.gz	37.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ts/3tsg ftp://data.pdbj.org/pub/pdb/validation_reports/ts/3tsg	HTTPS FTP

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Related structure data

Related structure data	3v3rC 2qpnS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5f83-2 6ts9-1 2zqa-d 3ni9-2 4h8r-2 6ts9-2 6q35-2 3v3r-2 4h8r-1 5f82-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 beta-lactamase GES-14

B: Extended-spectrum beta-lactamase GES-14

hetero molecules

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

1

A: Extended-spectrum beta-lactamase GES-14

hetero molecules

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

2

B: Extended-spectrum beta-lactamase GES-14

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.745, 84.098, 85.026
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 beta-lactamase GES-14 Mass: 31236.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaGES-14 / Plasmid: pet28a/blaGES-14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3X610, beta-lactamase
#2: Chemical	... ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.02 Å³/Da / Density % sol: 39.24 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Na iodide, 30 % PEG 3350, 5 % Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Jul 7, 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	Resolution: 1.9→19.61 Å / Num. all: 40716 / Num. obs: 40657 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / B_iso Wilson estimate: 18.3 Å² / R_sym value: 0.124 / Net I/σ(I): 11.6
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 5838 / R_sym value: 0.608 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASER		phasing
REFMAC	5.5.0110	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2QPN

2qpn

Resolution: 1.9→19.61 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.936 / SU B: 5.9 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20473	2042	5 %	RANDOM
R_work	0.16314	-	-	-
all	0.16525	40716	-	-
obs	0.16525	38560	99.85 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 21.629 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.07 Å²	0 Å²	0 Å²
2-	-	2.78 Å²	0 Å²
3-	-	-	0.28 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→19.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4060	0	121	280	4461

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	4428
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3102
X-RAY DIFFRACTION	r_angle_refined_deg	1.22	1.974	6025
X-RAY DIFFRACTION	r_angle_other_deg	0.865	3	7588
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.49	5	603
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.519	23.692	195
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.426	15	789
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.984	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	685
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4967
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	895
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	0.363	1.5	2748
X-RAY DIFFRACTION	r_mcbond_other	0.096	1.5	1124
X-RAY DIFFRACTION	r_mcangle_it	0.647	2	4458
X-RAY DIFFRACTION	r_scbond_it	1.19	3	1680
X-RAY DIFFRACTION	r_scangle_it	1.902	4.5	1529
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.236	133	-
R_work	0.212	2784	-
obs	-	2784	99.97 %

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	2.0728	0.0798	1.4425	0.7496	-0.0789	2.8298	-0.0697	0.1359	0.1557	-0.0886	-0.0228	0.1262	-0.093	-0.0826	0.0925	0.2553	0.0083	-0.0204	0.1225	0.0109	0.1666	30.928	23.515	3.339
2	1.2294	-0.5667	0.3842	0.7268	-0.3793	0.5471	0.0665	-0.2005	-0.1299	0.0408	0.0267	0.019	0.0657	-0.1053	-0.0932	0.282	-0.0156	-0.0039	0.0927	0.0221	0.1433	50.701	9.389	20.196
3	2.933	0.1406	0.3969	0.3955	-0.1352	0.5292	0.0666	-0.072	-0.2309	0.0293	-0.0129	0.0178	0.1072	-0.1487	-0.0537	0.2772	0.0042	-0.0264	0.0479	0.0199	0.1471	58.006	8.266	18.06
4	4.9007	-1.6685	-0.1983	3.2956	2.1792	4.2897	0.145	-0.2049	-0.368	-0.0538	-0.0044	0.1811	0.1653	-0.1022	-0.1407	0.2891	-0.0336	-0.0386	0.059	0.0691	0.1993	39.606	5.232	16.209
5	1.9358	0.2231	0.5174	0.5555	-0.1812	0.7657	-0.0071	-0.1176	0.1307	0.0291	-0.0394	0.0511	-0.0356	-0.0427	0.0465	0.227	0.002	-0.0145	0.0632	-0.004	0.1217	44.775	21.895	15.122
6	3.5874	-1.0552	-1.0397	4.4242	2.9977	6.5608	0.0321	-0.1411	0.3456	-0.0667	-0.0466	0.044	-0.2905	-0.0447	0.0145	0.1867	0.0043	-0.0375	0.0775	0.0226	0.142	41.821	24.516	10.193
7	2.5978	-0.2753	0.4151	2.1327	0.8343	3.0459	-0.0114	0.3741	0.1889	-0.2479	-0.0341	-0.0072	-0.025	0.1961	0.0455	0.2147	-0.008	-0.0336	0.1336	0.0239	0.0978	39.942	22.293	0.839
8	4.0416	-3.1555	2.1428	6.3786	-4.0529	1.7817	0.2553	0.5977	-0.0565	-0.1559	-0.3515	-0.1942	0.0811	0.2448	0.0963	0.3345	0.0308	0.021	0.173	-0.0607	0.1435	91.422	9.546	-1.325
9	2.2944	0.3981	-0.8735	1.6621	-0.3229	2.2409	0.0501	0.0379	0.1841	-0.0406	-0.1119	-0.1748	0.1286	0.2073	0.0618	0.2787	0.0037	-0.004	0.0382	-0.0286	0.1995	88.298	18.82	11.029
10	1.0117	-0.0481	-1.9681	2.42	0.2631	4.6021	-0.0503	-0.2953	0.2009	0.4008	0.1789	-0.1622	-0.1455	-0.0047	-0.1287	0.3478	0.0652	-0.0489	0.1319	-0.0641	0.2321	72.908	29.252	24.684
11	2.7277	-0.7709	-0.121	2.401	1.5275	1.8554	0.0504	0.1034	0.2265	-0.1782	-0.0275	0.1091	0.0189	-0.1509	-0.023	0.2715	-0.0123	-0.0047	0.0261	0.0078	0.1881	62.197	35.026	13.379
12	2.2302	-0.4465	0.4218	0.6591	0.2647	0.2573	-0.0443	0.0609	0.1678	0.0196	0.0443	-0.0257	-0.0017	0.0414	0	0.2753	0.0068	-0.0046	0.015	-0.0121	0.1566	66.735	31.275	15.095
13	3.3555	-0.7477	1.6813	3.1348	-0.4982	4.493	0.0956	0.2011	0.2061	-0.2711	0.0279	-0.3121	-0.0717	0.235	-0.1235	0.2799	0.0011	0.0341	0.0177	-0.0089	0.2661	82.714	32.917	9.255
14	1.6181	-0.1844	-0.0325	1.214	0.2003	0.7208	0.0267	0.0429	-0.0089	-0.0521	-0.0262	-0.0468	0.0453	0.0003	-0.0005	0.236	0.0081	-0.0058	0.0154	-0.006	0.1347	79.011	14.341	11.668

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	19 - 56
2	X-RAY DIFFRACTION	2	A	57 - 99
3	X-RAY DIFFRACTION	3	A	100 - 140
4	X-RAY DIFFRACTION	4	A	141 - 172
5	X-RAY DIFFRACTION	5	A	173 - 232
6	X-RAY DIFFRACTION	6	A	233 - 250
7	X-RAY DIFFRACTION	7	A	251 - 284
8	X-RAY DIFFRACTION	8	B	20 - 38
9	X-RAY DIFFRACTION	9	B	39 - 66
10	X-RAY DIFFRACTION	10	B	67 - 84
11	X-RAY DIFFRACTION	11	B	85 - 99
12	X-RAY DIFFRACTION	12	B	100 - 146
13	X-RAY DIFFRACTION	13	B	147 - 174
14	X-RAY DIFFRACTION	14	B	175 - 284

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