PDB-4u0t: Crystal structure of ADC-7 beta-lactamase

ID or keywords:

Entry

Database: PDB / ID: 4u0t

Title

Crystal structure of ADC-7 beta-lactamase

Components

ADC-7 beta-lactamase

Keywords

HYDROLASE / cephalosporinase /

beta-lactamase

Function / homology

Function and homology information

antibiotic catabolic process /

beta-lactamase activity /

beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.73 Å

Authors

Powers, R.A. / Wallar, B.J.

Citation

Journal: Biochemistry / Year: 2014
Title: Biochemical and Structural Analysis of Inhibitors Targeting the ADC-7 Cephalosporinase of Acinetobacter baumannii.
Authors: Powers, R.A. / Swanson, H.C. / Taracila, M.A. / Florek, N.W. / Romagnoli, C. / Caselli, E. / Prati, F. / Bonomo, R.A. / Wallar, B.J.

History

Deposition	Jul 14, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 24, 2014	Group: Database references
Revision 1.2	Feb 4, 2015	Group: Derived calculations
Revision 1.3	Sep 27, 2017	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Source and taxonomy Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4u0t.cif.gz	1.1 MB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u0/4u0t ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u0t	HTTPS FTP

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Related structure data

Related structure data	4u0xC C: citing same article (ref.)
Similar structure data	6tzf-4 4qd4-1 5chm-d 6tzf-1 5wae-1 6tzi-4 5wad-2 6pwl-1 6tzg-3 6tzi-3 4qd4-2 5wae-3 5w13-1 6tzj-2 6pwl-2 1l0d-1 5wac-1 5wag-2 6wif-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

4u0xC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#29 - May 2002 Penicillin-binding Proteins similarity (2)

Deposited unit

A: ADC-7 beta-lactamase

B: ADC-7 beta-lactamase

C: ADC-7 beta-lactamase

D: ADC-7 beta-lactamase

E: ADC-7 beta-lactamase

F: ADC-7 beta-lactamase

G: ADC-7 beta-lactamase

H: ADC-7 beta-lactamase

hetero molecules

326 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ADC-7 beta-lactamase

hetero molecules

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

2

B: ADC-7 beta-lactamase

hetero molecules

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

3

C: ADC-7 beta-lactamase

hetero molecules

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

4

D: ADC-7 beta-lactamase

hetero molecules

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

5

E: ADC-7 beta-lactamase

hetero molecules

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

6

F: ADC-7 beta-lactamase

hetero molecules

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

7

G: ADC-7 beta-lactamase

hetero molecules

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

8

H: ADC-7 beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.995, 88.571, 105.880
Angle α, β, γ (deg.)	67.29, 89.84, 89.40
Int Tables number	1
Space group name H-M	P1

#1: Protein	ADC-7 beta-lactamase Mass: 40677.301 Da / Num. of mol.: 8 / Fragment: UNP residues 24-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DRA1, beta-lactamase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1580 / 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: 2.19 Å³/Da / Density % sol: 43.8 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 1500, succinate, phosphate, glycine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.73→50 Å / Num. obs: 273490 / % possible obs: 97.3 % / Redundancy: 2.9 % / Net I/σ(I): 8.4

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Processing

Software

Name: REFMAC / Version: 5.7.0029 / Classification: refinement

Refinement

Resolution: 1.73→40 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.935 / SU B: 6.513 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23923	13803	5 %	RANDOM
R_work	0.19388	-	-	-
obs	0.19616	259682	95.67 %	-

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: 17.541 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.33 Å²	0.57 Å²	0.82 Å²
2-	-	0.41 Å²	-1.45 Å²
3-	-	-	0.23 Å²

Refinement step

Cycle: 1 / Resolution: 1.73→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21986	0	40	1580	23606

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	22724
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	21471
X-RAY DIFFRACTION	r_angle_refined_deg	2.032	1.964	30974
X-RAY DIFFRACTION	r_angle_other_deg	0.945	3	49474
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.803	5	2865
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.6	25.667	990
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.206	15	3759
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.281	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.123	0.2	3448
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	26028
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5116
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_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.73→1.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.321	860	-
R_work	0.272	14939	-
obs	-	-	74.79 %

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	0.9429	-0.0532	0.2585	0.5262	-0.0074	0.5842	-0.013	0.0472	0.1495	-0.0403	-0.046	0.004	0.0628	-0.0039	0.0589	0.0581	-0.0344	-0.0287	0.0544	0.06	0.0921	-12.7498	-1.7474	8.4646
2	0.9444	-0.0634	-0.4283	0.5072	-0.0105	0.5516	-0.0177	-0.0498	-0.1898	0.0385	-0.0498	0.0091	-0.0504	0.0111	0.0675	0.0518	-0.0392	-0.0463	0.0509	0.0644	0.1091	27.4511	-28.724	28.5435
3	2.856	0.7394	-0.1691	1.2111	0.0299	0.8993	0.0141	-0.1368	0.5019	0.0602	0.0514	0.4378	0.021	0.1499	-0.0655	0.0502	-0.0301	-0.033	0.0666	0.0488	0.3239	29.1219	15.5338	29.2434
4	2.5654	-0.9346	0.1127	1.4724	0.1297	0.7641	0.0237	0.131	-0.4545	-0.0783	0.0249	0.4916	-0.0205	0.1002	-0.0485	0.0422	-0.0336	-0.0661	0.0478	0.0424	0.3233	-11.8645	-45.8048	8.3665
5	0.7792	0.2398	-0.1898	0.5763	0.1626	2.4545	0.0837	-0.1766	0.0786	0.1277	0.1359	-0.0537	-0.1169	0.118	-0.2196	0.0659	-0.01	-0.0196	0.1502	-0.0216	0.0503	-17.3333	-7.4974	54.3289
6	0.919	-0.3353	-0.0101	0.6303	0.0724	2.6426	0.0986	0.243	-0.0915	-0.1664	0.1179	-0.0101	0.1673	0.1856	-0.2166	0.1193	-0.0278	-0.0612	0.2075	-0.048	0.0664	22.5061	-22.5772	-17.1457
7	1.2886	0.3176	0.5014	1.3871	0.7707	2.5043	0.0586	-0.1753	0.022	0.3904	0.0565	0.0224	0.3162	-0.1194	-0.115	0.1355	-0.0202	-0.0162	0.1024	0.0328	0.0211	-16.3177	-49.8868	52.8753
8	1.3399	-0.2387	-0.5046	1.0929	0.6151	2.0192	0.0507	0.237	-0.0083	-0.3232	0.0638	-0.0021	-0.225	-0.0369	-0.1145	0.1732	-0.0366	-0.0566	0.1321	0.0188	0.0587	24.7105	19.5817	-16.0355
9	0.175	0.0064	0.0229	0.0243	0.0098	0.0072	-0.0368	-0.0037	-0.0214	0.0361	0.0172	0.0406	-0.0017	0.0109	0.0196	0.2074	-0.0382	-0.0259	0.043	0.0641	0.1718	4.622	-15.1816	18.5632
10	0.2794	0.0467	0.0189	0.1109	-0.01	0.0835	-0.0017	0.0032	-0.0104	0.0054	-0.0013	0.0011	-0	0.0014	0.0031	0.0476	-0.0351	-0.0417	0.0519	0.0478	0.0489	6.4359	-14.9255	19.0096

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 358
2	X-RAY DIFFRACTION	2	B	1 - 358
3	X-RAY DIFFRACTION	3	C	6 - 357
4	X-RAY DIFFRACTION	4	D	6 - 357
5	X-RAY DIFFRACTION	5	E	5 - 358
6	X-RAY DIFFRACTION	6	F	3 - 358
7	X-RAY DIFFRACTION	7	G	6 - 356
8	X-RAY DIFFRACTION	8	H	6 - 356
9	X-RAY DIFFRACTION	9	A	401
10	X-RAY DIFFRACTION	9	B	401
11	X-RAY DIFFRACTION	9	C	401
12	X-RAY DIFFRACTION	9	D	401
13	X-RAY DIFFRACTION	9	E	401
14	X-RAY DIFFRACTION	9	F	401
15	X-RAY DIFFRACTION	9	G	401
16	X-RAY DIFFRACTION	9	H	401
17	X-RAY DIFFRACTION	10	A	501 - 822
18	X-RAY DIFFRACTION	10	B	501 - 835
19	X-RAY DIFFRACTION	10	C	501 - 661
20	X-RAY DIFFRACTION	10	D	501 - 663
21	X-RAY DIFFRACTION	10	E	501 - 680
22	X-RAY DIFFRACTION	10	F	501 - 657
23	X-RAY DIFFRACTION	10	G	501 - 623
24	X-RAY DIFFRACTION	10	H	501 - 639

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