PDB-8fqv: apo ADC-30 beta-lactamase

ID or keywords:

Entry

Database: PDB / ID: 8fqv

Title

apo ADC-30 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: 1.48 Å

Authors

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

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	Oct 25, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fqv.cif.gz	307.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8fqv.ent.gz	247.2 KB	Display	PDB format
PDBx/mmJSON format	8fqv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8fqv_validation.pdf.gz	433.7 KB	Display	wwPDB validaton report
Full document	8fqv_full_validation.pdf.gz	435.1 KB	Display
Data in XML	8fqv_validation.xml.gz	32.6 KB	Display
Data in CIF	8fqv_validation.cif.gz	50.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fq/8fqv ftp://data.pdbj.org/pub/pdb/validation_reports/fq/8fqv	HTTPS FTP

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Related structure data

Related structure data	8fqmC 8fqnC 8fqoC 8fqpC 8fqqC 8fqrC 8fqsC 8fqtC 8fquC 8fqwC 4u0xS 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	#29 - May 2002 Penicillin-binding Proteins similarity (2)

Deposited unit

B: Beta-lactamase

A: Beta-lactamase

hetero molecules

81.6 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)	43.154, 83.492, 205.332
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Beta-lactamase Mass: 40670.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaADC-30, AB237_1031 / Plasmid: pET 28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E1PRG7, beta-lactamase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.27 Å³/Da / Density % sol: 45.91 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: ADC-30 (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: 1.477→77.343 Å / Num. obs: 93283 / % possible obs: 90.7 % / Redundancy: 6.9 % / B_iso Wilson estimate: 19.43 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.086 / Net I/σ(I): 11.7
Reflection shell	Resolution: 1.477→1.58 Å / Redundancy: 7 % / Num. unique obs: 4664 / CC_1/2: 0.583 / % possible all: 58.6

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Processing

Software

Name	Version	Classification
PHENIX	v1.19.2	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4U0X

4u0x

Resolution: 1.48→36.85 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2062	4669	5.01 %
R_work	0.1717	-	-
obs	0.1734	93264	74.33 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.48→36.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5591	0	15	708	6314

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5811
X-RAY DIFFRACTION	f_angle_d	1.051	7912
X-RAY DIFFRACTION	f_dihedral_angle_d	13.104	2152
X-RAY DIFFRACTION	f_chiral_restr	0.09	870
X-RAY DIFFRACTION	f_plane_restr	0.008	1032

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 (%)
1.48-1.49	0.3531	13	0.3288	248	X-RAY DIFFRACTION	6
1.49-1.51	0.4585	26	0.3103	569	X-RAY DIFFRACTION	14
1.51-1.53	0.332	39	0.3063	751	X-RAY DIFFRACTION	19
1.53-1.55	0.3952	47	0.3058	980	X-RAY DIFFRACTION	25
1.55-1.57	0.3738	67	0.2861	1229	X-RAY DIFFRACTION	31
1.57-1.59	0.225	76	0.2604	1451	X-RAY DIFFRACTION	37
1.59-1.61	0.3556	67	0.2612	1575	X-RAY DIFFRACTION	40
1.61-1.64	0.3171	111	0.2664	1934	X-RAY DIFFRACTION	49
1.64-1.66	0.2765	110	0.252	2308	X-RAY DIFFRACTION	59
1.66-1.69	0.2902	149	0.2446	2648	X-RAY DIFFRACTION	68
1.69-1.72	0.2554	137	0.2471	2935	X-RAY DIFFRACTION	74
1.72-1.75	0.2497	169	0.2278	3193	X-RAY DIFFRACTION	82
1.75-1.78	0.2556	189	0.21	3441	X-RAY DIFFRACTION	87
1.78-1.82	0.249	221	0.2129	3756	X-RAY DIFFRACTION	96
1.82-1.86	0.2612	197	0.2127	3787	X-RAY DIFFRACTION	95
1.86-1.9	0.2652	188	0.2069	3883	X-RAY DIFFRACTION	98
1.9-1.95	0.2081	185	0.2048	3742	X-RAY DIFFRACTION	95
1.95-2	0.2225	199	0.1973	3555	X-RAY DIFFRACTION	90
2-2.06	0.2267	177	0.1807	3479	X-RAY DIFFRACTION	88
2.06-2.13	0.2169	210	0.1691	3901	X-RAY DIFFRACTION	99
2.13-2.21	0.195	247	0.1681	3845	X-RAY DIFFRACTION	98
2.21-2.29	0.1914	200	0.1669	3883	X-RAY DIFFRACTION	97
2.29-2.4	0.2051	182	0.1734	3948	X-RAY DIFFRACTION	98
2.4-2.53	0.227	203	0.1711	3939	X-RAY DIFFRACTION	99
2.53-2.68	0.2183	232	0.1786	3922	X-RAY DIFFRACTION	99
2.68-2.89	0.203	208	0.1782	3937	X-RAY DIFFRACTION	98
2.89-3.18	0.1951	219	0.1679	3918	X-RAY DIFFRACTION	98
3.18-3.64	0.187	207	0.1535	3786	X-RAY DIFFRACTION	93
3.64-4.59	0.1656	169	0.1245	3777	X-RAY DIFFRACTION	92
4.59-36.85	0.173	225	0.1496	4275	X-RAY DIFFRACTION	99

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	1.9855	-0.3144	-0.1914	1.5835	-0.4192	1.8112	0.0193	-0.0531	0.0977	0.211	0.0304	0.1416	-0.1115	-0.1314	-0.0406	0.1507	0.0023	0.0061	0.0786	-0.0034	0.1164	-20.0932	27.894	50.0528
2	2.0721	-0.1671	-0.4944	1.7033	0.1233	2.0363	-0.0438	0.2099	-0.1768	-0.221	-0.0549	-0.0527	0.1733	0.1496	0.0905	0.1937	0.0079	0.038	0.1628	-0.021	0.1073	-7.0573	2.1664	30.7776
3	0.8067	0.3474	-0.2639	1.4018	0.0672	0.8579	-0.023	0.186	-0.0296	-0.1437	0.0297	-0.0348	-0.0391	0.0093	-0.0067	0.1666	0.0028	0.0051	0.1582	0.004	0.1263	-14.5853	21.6246	35.4686
4	6.2129	-0.9218	0.4043	3.8462	-0.8486	6.2923	-0.046	0.2852	-0.0386	-0.2348	-0.3655	0.4619	0.1764	-0.8368	0.3932	0.1477	-0.0146	-0.0144	0.2416	-0.0728	0.1978	-28.4815	4.2795	37.1309
5	0.2267	-0.5027	0.1927	3.0351	-0.4575	0.6005	-0.0422	-0.0173	-0.031	0.1044	0.0085	-0.0047	0.0047	0.0191	0.0397	0.1151	-0.0062	0.0116	0.1103	0.0008	0.0886	-14.6578	8.4243	51.3891
6	1.8037	0.0161	-0.4033	1.9702	0.4481	1.4014	0.0355	-0.2064	-0.3329	0.1735	0.0416	-0.1282	0.3278	0.2301	-0.0597	0.1701	0.046	-0.0315	0.1356	0.0003	0.1724	-0.7863	-7.457	77.2762
7	2.0544	-0.3308	-0.2239	1.9648	0.7149	1.4565	0.0746	-0.3851	0.4234	-0.0087	-0.0099	0.0001	-0.3261	0.1185	-0.0544	0.1922	-0.0371	0.0241	0.2268	-0.0655	0.1689	-10.3513	23.3749	92.1625
8	2.9356	0.0607	-0.663	3.7434	-0.0989	2.6823	0.1074	0.1945	0.3891	-0.5834	-0.077	0.2661	-0.2919	-0.0641	-0.02	0.2194	0.0261	-0.0365	0.1751	-0.016	0.1718	-20.3381	21.6528	83.7453
9	1.1182	-0.0609	-0.3393	0.6648	0.4768	1.6325	0.08	-0.0754	0.094	-0.1038	0.0046	-0.0138	-0.1343	0.0865	-0.0842	0.1323	-0.0095	0.0054	0.136	0.0047	0.1066	-7.2488	13.1244	80.966
10	1.3677	-0.0445	-0.1801	1.2047	0.4488	1.5933	-0.0257	-0.7327	-0.0805	0.096	-0.0266	0.1126	0.1706	-0.0893	0.0077	0.1518	-0.0065	-0.0004	0.3115	0.0498	0.1085	-11.8621	4.9537	96.7333
11	1.8097	0.0921	-0.5328	1.952	0.8122	2.0537	0.0503	-0.3484	-0.3163	0.2586	-0.0032	-0.0178	0.3332	0.0585	-0.0561	0.153	0.0015	-0.0123	0.1581	0.0483	0.1187	-7.9692	-3.8532	86.618

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 62 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 63 through 176 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 177 through 239 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 240 through 256 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 257 through 359 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 2 through 62 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 63 through 105 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 106 through 136 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 137 through 239 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 240 through 307 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 308 through 358 )

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