PDB-6lc9: Crystal structure of AmpC Ent385 complex form with ceftazidime

ID or keywords:

Entry

Database: PDB / ID: 6lc9

Title

Crystal structure of AmpC Ent385 complex form with ceftazidime

Components

Beta-lactamase

Keywords

HYDROLASE /

BETA-LACTAMASE / CLASS C / AMPC /

ceftazidime

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

Enterobacter cloacae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.65 Å

Authors

Kawai, A. / Doi, Y.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01AI104895	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R21AI135522	United States

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2020
Title: Structural Basis of Reduced Susceptibility to Ceftazidime-Avibactam and Cefiderocol inEnterobacter cloacaeDue to AmpC R2 Loop Deletion.
Authors: Kawai, A. / McElheny, C.L. / Iovleva, A. / Kline, E.G. / Sluis-Cremer, N. / Shields, R.K. / Doi, Y.

History

Deposition	Nov 18, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2020	Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 8, 2020	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3	Mar 23, 2022	Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6lc9.cif.gz	344.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6lc9.ent.gz	240.6 KB	Display	PDB format
PDBx/mmJSON format	6lc9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lc/6lc9 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/6lc9	HTTPS FTP

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Related structure data

Related structure data	6lc7C 6lc8C C: citing same article (ref.)
Similar structure data	3gvb-1 3ixh-2 1iem-1 3gr2-1 3gtc-2 1my8-2 5w13-3 6wgq-1 2hdu-1 4jxs-2 3gsg-1 3grj-2 5chj-1 1ga9-1 1xgj-1 5ggw-1 6tzj-3 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

6lc7C

6lc8C

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 (3) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.389, 74.083, 102.822
Angle α, β, γ (deg.)	90.000, 94.786, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 2 molecules AB

#1: Protein	Beta-lactamase / Mass: 39444.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: CKO00_24250 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0Q7Z8*PLUS, beta-lactamase

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Non-polymers , 5 types, 612 molecules

#2: Chemical	ChemComp-CAZ / ACYLATED CEFTAZIDIME Mass: 469.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₁₉N₅O₇S₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₈O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Sequence details	First MET is derived from the plasmid vector. Authors have submitted the genome sequence of E. ...First MET is derived from the plasmid vector. Authors have submitted the genome sequence of E. cloacae Ent385 to the NCBI database and WGS and BioSample IDs are assigned as WNXG00000000 and SAMN13338939, respectively.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.26 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.8 M ammonium sulfate, 0.1 M MES pH 5.5 and 5% 1,4-Dioxane

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.65→46.7 Å / Num. obs: 89346 / % possible obs: 98.1 % / Redundancy: 7.1 % / B_iso Wilson estimate: 22.5 Å² / R_merge(I) obs: 0.057 / Net I/σ(I): 18.84
Reflection shell	Resolution: 1.65→1.75 Å / R_merge(I) obs: 0.773 / Num. unique obs: 14132

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.65→43.67 Å / SU ML: 0.2049 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.5733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1942	4467	5 %
R_work	0.1627	84854	-
obs	0.1642	89321	98.12 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→43.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5126	0	122	599	5847

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0089	5557
X-RAY DIFFRACTION	f_angle_d	0.9283	7604
X-RAY DIFFRACTION	f_chiral_restr	0.0666	821
X-RAY DIFFRACTION	f_plane_restr	0.0067	973
X-RAY DIFFRACTION	f_dihedral_angle_d	10.0649	3257

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 (%)
1.65-1.67	0.3677	145	0.299	2759	X-RAY DIFFRACTION	96.1
1.67-1.69	0.3151	147	0.2858	2793	X-RAY DIFFRACTION	96.05
1.69-1.71	0.3204	142	0.2637	2706	X-RAY DIFFRACTION	97.6
1.71-1.73	0.298	148	0.2531	2819	X-RAY DIFFRACTION	96.96
1.73-1.75	0.2518	146	0.2349	2769	X-RAY DIFFRACTION	96.75
1.75-1.77	0.237	147	0.2148	2798	X-RAY DIFFRACTION	97.84
1.77-1.8	0.259	147	0.1994	2792	X-RAY DIFFRACTION	96.17
1.8-1.83	0.2128	147	0.1923	2782	X-RAY DIFFRACTION	98.35
1.83-1.86	0.2015	149	0.1844	2834	X-RAY DIFFRACTION	97.55
1.86-1.89	0.1884	147	0.1688	2787	X-RAY DIFFRACTION	97.25
1.89-1.92	0.2178	147	0.1718	2801	X-RAY DIFFRACTION	98.04
1.92-1.95	0.1973	149	0.1673	2833	X-RAY DIFFRACTION	97.39
1.95-1.99	0.1959	148	0.1615	2804	X-RAY DIFFRACTION	98.24
1.99-2.03	0.1787	147	0.1588	2800	X-RAY DIFFRACTION	97.65
2.03-2.08	0.1724	149	0.1577	2828	X-RAY DIFFRACTION	98.41
2.08-2.12	0.1683	149	0.1531	2818	X-RAY DIFFRACTION	98.02
2.12-2.18	0.1896	149	0.156	2841	X-RAY DIFFRACTION	98.29
2.18-2.24	0.1793	150	0.1493	2846	X-RAY DIFFRACTION	98.52
2.24-2.3	0.2031	149	0.1571	2842	X-RAY DIFFRACTION	98.13
2.3-2.38	0.1832	149	0.1602	2821	X-RAY DIFFRACTION	98.8
2.38-2.46	0.2095	149	0.1612	2838	X-RAY DIFFRACTION	98.74
2.46-2.56	0.1789	150	0.1618	2852	X-RAY DIFFRACTION	98.72
2.56-2.68	0.2006	149	0.1633	2831	X-RAY DIFFRACTION	98.81
2.68-2.82	0.1823	152	0.1673	2872	X-RAY DIFFRACTION	98.99
2.82-2.99	0.2331	151	0.1695	2870	X-RAY DIFFRACTION	99.15
2.99-3.22	0.1832	151	0.1621	2871	X-RAY DIFFRACTION	99.38
3.22-3.55	0.1797	152	0.1516	2880	X-RAY DIFFRACTION	99.38
3.55-4.06	0.1483	152	0.1333	2902	X-RAY DIFFRACTION	99.48
4.06-5.12	0.1751	153	0.1322	2909	X-RAY DIFFRACTION	99.54
5.12-43.67	0.216	157	0.179	2956	X-RAY DIFFRACTION	99.23

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	6.64788825838	3.08429276285	0.30531362245	4.24458254189	0.253629439364	2.55314672701	-0.0828454256109	-0.675618765552	-0.72529967508	0.228951983642	-0.0303341216992	-1.0267906419	0.270225426314	0.527423039779	0.0833089658327	0.26542551008	0.100414828504	-0.048417697298	0.362247982826	0.0385505682316	0.400643477109	23.7271973811	-14.6651274013	17.7809342599
2	1.07090567319	-0.425163491163	-0.234157636087	1.37451674624	0.107586519322	1.14410319193	0.00866825202115	0.000169493384	-0.0166623814732	-0.0359601551859	0.0141715041118	0.0189790463258	-0.0504913527355	0.0846499770206	-0.0252013950353	0.089559143451	-0.0213830817524	-0.0069766226628	0.124099552674	0.00287899636771	0.102400512343	8.41224880772	2.27845432586	10.1161560928
3	4.34802836689	0.0867145133067	-0.0173992339204	1.40780704995	-0.225561847282	3.83145670929	0.0798469969812	-0.043070226755	0.0479155769805	0.0255277546676	-0.0203037979883	0.125392029739	-0.113376626949	-0.287484442323	-0.0517547128768	0.118070813586	0.0246758484923	0.00807208731415	0.138937468954	-0.00167799581795	0.135212508328	-10.5497789154	8.89885259529	18.1307205839
4	2.65839013455	-3.01308372346	-0.741076886599	6.11615234889	1.54202749157	2.4429672003	0.111277765106	0.309300330023	0.0256975847049	-0.280029977715	-0.121349052487	0.192518809972	-0.0752334207549	-0.0164617891626	0.00650990247225	0.220114989775	-0.0157506228623	0.00404381842179	0.199026891645	0.0301366345392	0.137970330257	5.90567476309	9.49895045595	1.74854058828
5	1.74193889409	-0.246876737259	-0.104758155713	1.11522595305	0.730562769365	1.9463184459	0.0379128637275	-0.165268944595	0.0154865572074	0.00789465842424	-0.0125627909294	-0.0518930813304	-0.00987758307625	0.0987645938967	-0.0165508400562	0.101082853432	-0.00993124758561	-0.00788599164423	0.159188668314	0.0157752935245	0.13248504036	8.73153594795	2.44003784034	14.2959556939
6	9.7881143589	1.46967835664	-2.98035339589	5.13592713814	-0.771841788096	2.63524433384	-0.115884436792	-0.562557357908	-0.013943778284	0.0877286180099	0.235769207115	0.357372398618	0.21313694355	-0.0793186845172	-0.123415202337	0.255993854012	-0.0109686578841	-0.0542627666246	0.392694196791	-0.0241283574741	0.0969745706057	3.82928963819	8.72588668109	28.9929221894
7	2.3661328981	1.03026166454	0.436836105273	2.93277064667	1.07402977608	1.84854846043	-0.0250166208657	-0.331672370972	-0.0797432003639	0.0913535111897	0.0181261408497	-0.178812177185	0.0202806105883	0.262117174268	-0.0131003417543	0.124287905427	-0.000482913628951	-0.0192807890177	0.235675783316	0.0307668280903	0.140862822527	14.686709215	-4.0058798293	20.485636254
8	7.79609594913	5.22736752115	-3.91047226487	6.78447323134	-2.882589881	6.46577297406	0.291459023442	0.499546014644	0.797043424076	0.195628035014	0.1343653784	0.939258862993	-0.212373429995	-0.791980973765	-0.424945730236	0.261823161677	0.0505501572906	-0.00771981701593	0.317060012058	0.0494570251417	0.350097175258	-9.62543229347	-14.2913200739	34.1918525428
9	1.16022805852	-0.525207837574	0.917502660741	0.707017856353	-0.82134873778	2.46221103356	0.0372009236138	0.0368007849634	-0.103648182323	-0.0469747507074	-0.00394219006448	0.0688510514685	0.161300233709	0.00652468259621	-0.0367932848491	0.210107438389	-0.0282504758448	-0.00567285669783	0.184966898811	0.0172529308431	0.227154738735	4.87591713055	-30.5058253745	44.1807238641
10	6.53526683012	-0.636645190944	-2.61878410237	3.31047601939	-0.560884257989	3.47411605373	-0.20233816642	0.414136979653	0.169647225891	-0.237157925854	0.0543481192589	-0.123357209037	-0.0491061855267	0.353112412064	0.170872216822	0.20835153818	-0.0865191048091	-0.0431348405036	0.346570413993	0.063069535252	0.205830512897	25.0552111922	-29.6273796626	56.7554319482
11	7.00348419382	-3.74004327612	-2.02739013151	2.44202941907	0.19648754367	2.39555130807	0.1173574253	-0.110033216758	0.330326354088	-0.0969573892271	-0.344509457305	-0.34636635907	-0.118067182068	0.460968980794	0.236510333149	0.273570977077	-0.0410564293021	-0.0493010065885	0.335136930296	0.0802075202071	0.281393708503	18.8486834818	-30.4562535884	53.2690191815
12	0.944960684904	-0.172657913845	0.251299269243	0.45147318602	-0.606048970818	2.27770854616	-5.50620845884E-5	0.00394928448649	-0.0709079777902	-0.0270464838954	0.00129564344329	0.0519652198557	0.0456995776471	-0.00795939022035	0.00202100349237	0.206648959062	-0.0213030212807	-0.00890105490108	0.210491903347	0.0317951304612	0.262492164488	3.21688197046	-27.132742002	46.8213039328

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 98 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 99 through 162 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 163 through 192 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 193 through 285 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 286 through 308 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 309 through 358 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 3 through 23 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 24 through 98 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 99 through 136 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 137 through 162 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 163 through 358 )

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