PDB-8fqp: apo ADC-162 beta-lactamase

ID or keywords:

Entry

Database: PDB / ID: 8fqp

Title

apo ADC-162 beta-lactamase

Components

Beta-lactamase

Keywords

HYDROLASE / Acinetobacter-derived Cephalosporinase

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 /

MOLECULAR REPLACEMENT / Resolution: 1.419 Å

Authors

Powers, R.A. / Wallar, B.J. / June, C.M. / Fernando, M.C.

Funding support

United States, 1items

Citation

Journal: J.Med.Chem. / Year: 2023
Title: Synthesis of a Novel Boronic Acid Transition State Inhibitor, MB076: A Heterocyclic Triazole Effectively Inhibits Acinetobacter -Derived Cephalosporinase Variants with an Expanded-Substrate Spectrum.
Authors: Powers, R.A. / June, C.M. / Fernando, M.C. / Fish, E.R. / Maurer, O.L. / Baumann, R.M. / Beardsley, T.J. / Taracila, M.A. / Rudin, S.D. / Hujer, K.M. / Hujer, A.M. / Santi, N. / Villamil, V. ...

History

Deposition	Jan 6, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 12, 2023	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 26, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8fqp.cif.gz	302.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8fqp.ent.gz	243.7 KB	Display	PDB format
PDBx/mmJSON format	8fqp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8fqp_validation.pdf.gz	456.9 KB	Display	wwPDB validaton report
Full document	8fqp_full_validation.pdf.gz	459 KB	Display
Data in XML	8fqp_validation.xml.gz	32 KB	Display
Data in CIF	8fqp_validation.cif.gz	48.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fq/8fqp ftp://data.pdbj.org/pub/pdb/validation_reports/fq/8fqp	HTTPS FTP

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Related structure data

Related structure data	8fqmC 8fqnC 8fqoC 8fqqC 8fqrC 8fqsC 8fqtC 8fquC 8fqvC 8fqwC 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	#29 - May 2002 Penicillin-binding Proteins similarity (2) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

B: Beta-lactamase

A: Beta-lactamase

hetero molecules

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

1

B: Beta-lactamase

hetero molecules

defined by author
Evidence: monomeric biologic assembly
40.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	43.054, 83.633, 204.338
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta-lactamase Mass: 40728.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaADC / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2H4PPJ8
#2: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.53 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: ADC-162 (3.5 mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/ phosphate/ glycine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.419→77.401 Å / Num. obs: 109418 / % possible obs: 93.5 % / Redundancy: 5.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.078 / R_pim(I) all: 0.035 / Net I/σ(I): 10.8
Reflection shell	Resolution: 1.419→1.536 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.74 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5467 / CC_1/2: 0.648 / R_pim(I) all: 0.344 / % possible all: 50.6

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Processing

Software

Name	Version	Classification
Aimless	V0.7.4	data scaling
PHASER		phasing
PHENIX	v1.19.2	refinement
autoPROC	v1.0.5	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.419→38.7 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2185	5433	4.97 %	0.5
R_work	0.186	-	-	-
obs	0.1876	109418	76.5 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.419→38.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5540	0	15	590	6145

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5766
X-RAY DIFFRACTION	f_angle_d	0.992	7858
X-RAY DIFFRACTION	f_dihedral_angle_d	13.26	2121
X-RAY DIFFRACTION	f_chiral_restr	0.089	871
X-RAY DIFFRACTION	f_plane_restr	0.007	1027

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 (%)
1.419-1.43	0.3985	18	0.283	246	X-RAY DIFFRACTION	6
1.43-1.44	0.2951	15	0.2927	331	X-RAY DIFFRACTION	7
1.44-1.46	0.2915	25	0.284	450	X-RAY DIFFRACTION	10
1.46-1.48	0.2788	38	0.2549	640	X-RAY DIFFRACTION	14
1.48-1.5	0.2773	63	0.2586	895	X-RAY DIFFRACTION	20
1.5-1.52	0.3114	92	0.26	1362	X-RAY DIFFRACTION	31
1.52-1.54	0.3061	107	0.2409	1877	X-RAY DIFFRACTION	42
1.54-1.56	0.2428	142	0.2397	2437	X-RAY DIFFRACTION	56
1.56-1.59	0.2706	164	0.2349	3064	X-RAY DIFFRACTION	68
1.59-1.61	0.2613	161	0.2334	3453	X-RAY DIFFRACTION	77
1.61-1.64	0.2542	173	0.2356	3805	X-RAY DIFFRACTION	83
1.64-1.67	0.2475	210	0.2283	4067	X-RAY DIFFRACTION	91
1.67-1.7	0.2577	218	0.2345	4381	X-RAY DIFFRACTION	97
1.7-1.74	0.2748	229	0.2464	4456	X-RAY DIFFRACTION	99
1.74-1.78	0.3174	212	0.2241	4510	X-RAY DIFFRACTION	100
1.78-1.82	0.239	248	0.2056	4498	X-RAY DIFFRACTION	100
1.82-1.86	0.2805	239	0.1999	4481	X-RAY DIFFRACTION	100
1.86-1.91	0.2188	227	0.2031	4489	X-RAY DIFFRACTION	100
1.91-1.97	0.2231	235	0.1987	4552	X-RAY DIFFRACTION	100
1.97-2.03	0.2183	233	0.1923	4494	X-RAY DIFFRACTION	100
2.03-2.11	0.2116	238	0.1889	4466	X-RAY DIFFRACTION	99
2.11-2.19	0.2374	259	0.1864	4493	X-RAY DIFFRACTION	99
2.19-2.29	0.2098	228	0.1819	4529	X-RAY DIFFRACTION	100
2.29-2.41	0.2407	222	0.1887	4577	X-RAY DIFFRACTION	100
2.41-2.56	0.2243	238	0.1965	4528	X-RAY DIFFRACTION	100
2.56-2.76	0.254	232	0.1985	4559	X-RAY DIFFRACTION	100
2.76-3.04	0.2229	224	0.1944	4607	X-RAY DIFFRACTION	99
3.04-3.48	0.2167	243	0.1801	4566	X-RAY DIFFRACTION	99
3.48-4.38	0.1749	245	0.1447	4485	X-RAY DIFFRACTION	96
4.38-38.7	0.1668	255	0.1511	4687	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	1.0029	0.307	-0.1948	1.6221	-0.0177	1.1595	-0.0397	-0.1087	-0.0448	0.0329	-0.0043	-0.1127	0.136	0.0341	0.0551	0.104	0.0235	-0.0107	0.0841	-0.0156	0.0835	-4.6535	16.3779	-41.579
2	2.3047	0.0797	0.2721	1.6096	0.9263	3.3892	-0.131	-0.3336	-0.0524	0.2416	-0.1649	0.2285	0.1123	-0.3644	0.2647	0.2428	-0.01	0.0345	0.1815	0.0086	0.149	-16.6825	3.0337	-31.4329
3	1.0687	-0.9787	0.1567	2.1532	-0.3	0.8998	-0.0209	-0.1466	-0.0618	0.1897	0.0286	0.0128	0.0373	0.0192	-0.0181	0.1475	-0.0034	-0.0075	0.1416	-0.0138	0.1261	-4.0417	17.6761	-35.4781
4	0.1816	0.4854	0.2646	2.8671	0.2832	0.3913	-0.0685	-0.0115	-0.0322	-0.0421	0.0441	-0.0087	0.0387	0.0046	0.0367	0.0975	0.0091	0.01	0.082	-0.0026	0.0861	-6.916	8.148	-51.0321
5	1.1274	-0.008	-0.2189	1.5243	-0.6611	1.488	0.0254	0.1695	-0.2071	-0.1448	0.0474	0.126	0.2441	-0.2211	-0.0502	0.121	-0.0255	-0.0292	0.1545	-0.0125	0.1385	-19.6754	-3.3492	-79.5716
6	2.9143	-0.5572	-0.1029	2.3521	0.1768	1.4821	0.067	0.2065	0.3929	0.2556	-0.0366	-0.1172	-0.3005	0.06	-0.0272	0.1737	-0.0067	0.0071	0.1422	0.0618	0.1593	-3.4087	22.8738	-88.3709
7	1.0741	-0.311	0.2021	1.1123	-0.9029	2.2783	0.0302	0.1835	0.0537	0.0458	0.0499	0.0915	-0.1484	-0.2364	-0.0695	0.0917	0.013	0.0147	0.167	0.0113	0.1043	-19.9307	10.0645	-81.0449
8	1.8362	0.56	-0.4592	1.3151	-1.0029	0.9314	-0.0288	0.4296	-0.1401	-0.2009	-0.0405	-0.1068	0.1415	0.073	0.0625	0.136	0.0348	0.003	0.2529	-0.046	0.1312	-6.3068	2.2636	-93.4908
9	1.7752	0.002	0.0861	2.2068	0.178	3.0535	0.0274	0.3637	-0.4618	-0.3341	0.0316	-0.0179	0.405	-0.0363	-0.0882	0.1903	-0.0114	-0.0177	0.1544	-0.0596	0.162	-13.3601	-6.8174	-85.9247

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 105 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 106 through 176 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 177 through 256 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 257 through 401 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 2 through 79 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 80 through 166 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 167 through 256 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 257 through 326 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 327 through 401 )

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