PDB-7qor: Structure of beta-lactamase TEM-171

ID or keywords:

Entry

Database: PDB / ID: 7qor

Title

Structure of beta-lactamase TEM-171

Components

Beta-lactamase TEM

Keywords

HYDROLASE / BETA-LACTAMASE

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.999 Å

Authors

Hakanpaa, J. / Petrova, T. / Samygina, V.R. / Chojnowski, G. / Lamzin, V. / Egorov, A.M.

Funding support

European Union, 3items

Organization	Grant number	Country
Russian Science Foundation	15-14-00014-C	European Union
German Federal Ministry for Education and Research	05K10YEA	European Union
European Commission	H2020-EINFRA-2015-1-675858	European Union

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Crystal structures of the molecular class A beta-lactamase TEM-171 and its complexes with tazobactam.
Authors: Grigorenko, V.G. / Petrova, T.E. / Carolan, C. / Rubtsova, M.Y. / Uporov, I.V. / Pereira, J. / Chojnowski, G. / Samygina, V.R. / Lamzin, V.S. / Egorov, A.M.

History

Deposition	Dec 28, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7qor.cif.gz	592.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7qor.ent.gz		Display	PDB format
PDBx/mmJSON format	7qor.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7qor_validation.pdf.gz	490.7 KB	Display	wwPDB validaton report
Full document	7qor_full_validation.pdf.gz	509 KB	Display
Data in XML	7qor_validation.xml.gz	64 KB	Display
Data in CIF	7qor_validation.cif.gz	90.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qo/7qor ftp://data.pdbj.org/pub/pdb/validation_reports/qo/7qor	HTTPS FTP

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Related structure data

Related structure data	7qlpC 7qnkC 3jyiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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 (6) #29 - May 2002 Penicillin-binding Proteins similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

AAA: Beta-lactamase TEM

BBB: Beta-lactamase TEM

CCC: Beta-lactamase TEM

DDD: Beta-lactamase TEM

EEE: Beta-lactamase TEM

FFF: Beta-lactamase TEM

hetero molecules

174 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Beta-lactamase TEM

hetero molecules

defined by author
Evidence: gel filtration
29.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Beta-lactamase TEM

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

3

CCC: Beta-lactamase TEM

hetero molecules

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

4

DDD: Beta-lactamase TEM

hetero molecules

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

5

EEE: Beta-lactamase TEM

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

6

FFF: Beta-lactamase TEM

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

Unit cell

Length a, b, c (Å)	88.190, 88.190, 499.323
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	EEE-487- HOH

#1: Protein	Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2 Mass: 28956.021 Da / Num. of mol.: 6 / Mutation: V84I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.79 Å³/Da / Density % sol: 55.98 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: PEG-4000, 0.2 M calcium acetate, 0.1 M Tris-HCl, pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.999→86.85 Å / Num. obs: 132474 / % possible obs: 98.6 % / Redundancy: 13.2 % / CC_1/2: 0.99 / Net I/σ(I): 18.5
Reflection shell	Resolution: 1.999→2.05 Å / Num. unique obs: 9279 / CC_1/2: 0.787

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3JYI

3jyi

Resolution: 1.999→15 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.958 / SU B: 8.843 / SU ML: 0.128 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2106	6526	4.942 %
R_work	0.1899	125525	-
all	0.191	-	-
obs	-	132051	97.834 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 58.018 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.363 Å²	-0 Å²	-0 Å²
2-	-	1.363 Å²	-0 Å²
3-	-	-	-2.727 Å²

Refinement step

Cycle: LAST / Resolution: 1.999→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12168	0	32	875	13075

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	12443
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	11842
X-RAY DIFFRACTION	r_angle_refined_deg	1.558	1.645	16856
X-RAY DIFFRACTION	r_angle_other_deg	1.356	1.575	27432
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.406	5	1582
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.463	21.484	647
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.932	15	2211
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.345	15	109
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	1673
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	13952
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2515
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	2548
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	10928
X-RAY DIFFRACTION	r_nbtor_refined	0.153	0.2	6108
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	5488
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	787
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.044	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.094	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.229	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.219	0.2	29
X-RAY DIFFRACTION	r_mcbond_it	1.17	1.849	6323
X-RAY DIFFRACTION	r_mcbond_other	1.17	1.848	6321
X-RAY DIFFRACTION	r_mcangle_it	1.901	2.761	7892
X-RAY DIFFRACTION	r_mcangle_other	1.901	2.762	7893
X-RAY DIFFRACTION	r_scbond_it	1.448	2.113	6120
X-RAY DIFFRACTION	r_scbond_other	1.448	2.114	6121
X-RAY DIFFRACTION	r_scangle_it	2.418	3.087	8960
X-RAY DIFFRACTION	r_scangle_other	2.418	3.088	8961
X-RAY DIFFRACTION	r_lrange_it	7.314	22.933	14110
X-RAY DIFFRACTION	r_lrange_other	7.257	22.264	13889

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.999-2.05	0.323	438	0.316	8841	0.316	9677	0.677	0.68	95.8872	0.28
2.05-2.105	0.32	445	0.291	8698	0.292	9375	0.756	0.775	97.5253	0.256
2.105-2.165	0.255	425	0.261	8520	0.261	9163	0.864	0.856	97.6209	0.226
2.165-2.23	0.254	423	0.249	8265	0.249	8901	0.885	0.883	97.607	0.211
2.23-2.301	0.254	431	0.224	8012	0.226	8634	0.895	0.912	97.7878	0.188
2.301-2.38	0.23	411	0.213	7840	0.214	8418	0.927	0.929	98.0162	0.18
2.38-2.468	0.238	390	0.198	7564	0.2	8106	0.931	0.943	98.1248	0.165
2.468-2.566	0.209	377	0.187	7307	0.188	7815	0.942	0.948	98.3237	0.157
2.566-2.676	0.207	356	0.183	7086	0.184	7565	0.943	0.948	98.3741	0.157
2.676-2.802	0.234	366	0.186	6697	0.189	7188	0.936	0.947	98.261	0.163
2.802-2.948	0.223	353	0.184	6506	0.186	6952	0.945	0.953	98.6623	0.163
2.948-3.119	0.219	335	0.196	6113	0.197	6558	0.944	0.949	98.3227	0.18
3.119-3.325	0.201	313	0.202	5792	0.202	6177	0.954	0.954	98.8344	0.191
3.325-3.576	0.212	294	0.201	5478	0.201	5835	0.961	0.96	98.9203	0.195
3.576-3.896	0.221	253	0.187	5102	0.188	5405	0.95	0.96	99.0749	0.185
3.896-4.319	0.189	245	0.157	4660	0.159	4942	0.965	0.97	99.2513	0.161
4.319-4.92	0.144	240	0.144	4209	0.144	4477	0.979	0.978	99.3746	0.151
4.92-5.87	0.178	176	0.168	3683	0.168	3886	0.975	0.978	99.3052	0.172
5.87-7.73	0.229	143	0.197	3028	0.198	3181	0.955	0.967	99.6856	0.206
7.73-15	0.18	112	0.145	2124	0.146	2278	0.973	0.982	98.1563	0.164

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	1.1981	-0.0988	0.7094	0.0479	0.0638	1.5345	0.2201	0.1984	0.0264	0.0093	-0.127	-0.0084	-0.0649	0.1366	-0.0931	0.2698	-0.0201	0.0494	0.6619	0.0267	0.2995	-5.629	-17.344	61.632
2	1.8747	-0.0681	1.6104	0.2265	-0.3522	2.46	0.5218	-0.1598	-0.0915	0.0728	-0.2654	-0.0423	-0.0789	0.0252	-0.2564	0.4128	0.0613	0.1114	1.0545	0.206	0.1135	-18.474	27.057	61.128
3	0.8345	0.5108	-0.5505	0.3285	-0.3047	1.5694	0.0312	0.0889	0.0083	0.0767	-0.0268	-0.0119	0.0518	-0.0573	-0.0044	0.3488	-0.1653	0.0316	0.5195	-0.0188	0.333	-24.315	-20.772	103.035
4	1.171	0.6433	0.9818	0.3755	0.5092	2.4817	0.0869	0.1391	0.059	0.0979	0.0164	0.0925	0.0753	0.1149	-0.1033	0.4113	-0.2164	-0.01	0.4588	0.0304	0.3024	9.152	10.395	105.85
5	0.8705	0.1677	0.5591	0.1451	-0.3254	2.0642	0.1181	-0.0596	-0.0574	0.018	0.032	0.0268	0.0977	-0.3396	-0.1502	0.3096	-0.2384	-0.0014	0.7021	0.082	0.2922	21.713	-36.095	104.767
6	2.7863	1.1432	-3.2929	0.7305	-1.6253	4.2946	0.8994	-0.525	-0.0788	0.4613	-0.6316	0.1389	-1.3023	0.8337	-0.2678	0.6073	-0.371	0.1375	1.2642	-0.0119	0.2709	-37.349	25.102	102.528

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	26 - 501
2	X-RAY DIFFRACTION	2	ALL	BBB	26 - 290
3	X-RAY DIFFRACTION	3	ALL	CCC	26 - 501
4	X-RAY DIFFRACTION	4	ALL	DDD	26 - 501
5	X-RAY DIFFRACTION	5	ALL	EEE	26 - 501
6	X-RAY DIFFRACTION	6	ALL	FFF	26 - 290

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