PDB-4kz6: Crystal structure of AmpC beta-lactamase in complex with fragment...

ID or keywords:

Entry

Database: PDB / ID: 4kz6

Title

Crystal structure of AmpC beta-lactamase in complex with fragment 13 ((2R,6R)-6-methyl-1-(3-sulfanylpropanoyl)piperidine-2-carboxylic acid)

Components

Beta-lactamase

Keywords

HYDROLASE/HYDROLASE INHIBITOR / AMPC beta-lactamase / class C /

hydrolase / cephalosporinase / HYDROLASE-HYDROLASE INHIBITOR complex

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

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

Eidam, O. / Barelier, S. / Fish, I. / Shoichet, B.K.

Citation

Journal: Acs Chem.Biol. / Year: 2014
Title: Increasing chemical space coverage by combining empirical and computational fragment screens.
Authors: Barelier, S. / Eidam, O. / Fish, I. / Hollander, J. / Figaroa, F. / Nachane, R. / Irwin, J.J. / Shoichet, B.K. / Siegal, G.

History

Deposition	May 29, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 21, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 30, 2014	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4kz6.cif.gz	301.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kz/4kz6 ftp://data.pdbj.org/pub/pdb/validation_reports/kz/4kz6	HTTPS FTP

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Related structure data

Related structure data	4kz3C 4kz4C 4kz5C 4kz7C 4kz8C 4kz9C 4kzaC 4kzbC 1ke4S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4jxw-1 5ggw-1 3gvb-1 6x9y-1 1fco-2 4e3k-2 3fkv-1 4okp-2 1my8-2 1kds-2 4old-1 6dpx-2 4e3m-2 4kz3-1 3gr2-1 1l0e-2 4kg6-4 1kdw-2 1ke4-2 3bls-2 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

C: citing same article (ref.)

S: Starting model for refinement

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: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	118.090, 77.080, 97.540
Angle α, β, γ (deg.)	90.000, 116.360, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Beta-lactamase / / AmpC beta-lactamase / Cephalosporinase Mass: 39587.922 Da / Num. of mol.: 2 / Fragment: UNP residues 20-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-ZB6 / (2R,6R)-6-methyl-1-(3-sulfanylpropanoyl)piperidine-2-carboxylic acid Mass: 231.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₇NO₃S
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 753 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 51.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 1.7 M potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 80 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 1.115869 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2012

Radiation

Monochromator: KHOZU Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.115869 Å / Relative weight: 1

Reflection

Resolution: 1.68→29.516 Å / Num. obs: 89087 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 30.447 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 19.36

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.68-1.72		0.491	2.58	26275	6543	99.8
1.72-1.77		0.391	3.31	26001	6397	99.8
1.77-1.82		0.298	4.38	25738	6262	99.8
1.82-1.88		0.246	5.34	24776	6007	99.8
1.88-1.94		0.18	7.47	24617	5896	99.7
1.94-2.01		0.14	9.58	23770	5662	99.7
2.01-2.08		0.106	12.38	23029	5475	99.7
2.08-2.17		0.085	15.29	22163	5256	99.8
2.17-2.27		0.072	18.46	21430	5095	99.8
2.27-2.38		0.063	20.51	20071	4800	99.4
2.38-2.5		0.052	24.12	19498	4633	99.7
2.5-2.66		0.046	27.15	18151	4336	99.7
2.66-2.84		0.038	31.26	17113	4104	99.6
2.84-3.07		0.032	36.28	15847	3826	99.6
3.07-3.36		0.028	41.64	14543	3544	99.6
3.36-3.76		0.026	45.34	12678	3162	99.8
3.76-4.34		0.023	48.28	11491	2819	99.6
4.34-5.31		0.021	50.44	10197	2395	99.8
5.31-7.51		0.021	49.41	7940	1875	99.6
	7.51	0.02	50.95	4007	1000	93.7

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KE4

1ke4

Resolution: 1.68→29.516 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.879 / SU ML: 0.17 / σ(F): 1.99 / Phase error: 19.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1785	3251	3.65 %
R_work	0.1543	-	-
obs	0.1552	89077	99.8 %

Solvent computation

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

Displacement parameters

B_iso max: 73.35 Å² / B_iso mean: 22.6947 Å² / B_iso min: 6.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→29.516 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5503	0	40	753	6296

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	5715
X-RAY DIFFRACTION	f_angle_d	1.452	7837
X-RAY DIFFRACTION	f_chiral_restr	0.099	859
X-RAY DIFFRACTION	f_plane_restr	0.007	1007
X-RAY DIFFRACTION	f_dihedral_angle_d	12.851	2032

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.68-1.7051	0.2622	153	0.2169	3682	3835	100
1.7051-1.7317	0.2446	90	0.2136	3790	3880	100
1.7317-1.7601	0.2329	142	0.2046	3716	3858	100
1.7601-1.7904	0.2398	151	0.2014	3676	3827	100
1.7904-1.823	0.2269	138	0.1878	3732	3870	100
1.823-1.8581	0.2305	139	0.1841	3727	3866	100
1.8581-1.896	0.2174	100	0.1896	3750	3850	100
1.896-1.9372	0.2097	120	0.1856	3730	3850	100
1.9372-1.9822	0.2184	154	0.181	3707	3861	100
1.9822-2.0318	0.2276	135	0.1748	3734	3869	100
2.0318-2.0867	0.2018	142	0.1625	3727	3869	100
2.0867-2.1481	0.2025	157	0.1626	3702	3859	100
2.1481-2.2174	0.2023	152	0.1602	3736	3888	100
2.2174-2.2967	0.199	131	0.1585	3718	3849	100
2.2967-2.3886	0.2251	145	0.1574	3698	3843	100
2.3886-2.4972	0.1827	131	0.1578	3782	3913	100
2.4972-2.6288	0.2036	147	0.1594	3714	3861	100
2.6288-2.7934	0.1749	155	0.1578	3713	3868	100
2.7934-3.0089	0.1698	163	0.1588	3725	3888	100
3.0089-3.3113	0.1754	155	0.152	3736	3891	100
3.3113-3.7896	0.14	139	0.1304	3768	3907	100
3.7896-4.7712	0.1399	170	0.118	3750	3920	100
4.7712-29.5207	0.1486	142	0.1482	3813	3955	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	1.9098	0.7602	-0.4764	1.2258	-0.1261	1.1117	0.0416	-0.2556	-0.0376	0.227	-0.0999	0.1385	0.2428	-0.121	0.0452	0.2141	-0.0574	0.0164	0.1182	-0.0194	0.1102	21.5096	-9.6697	24.3803
2	1.7072	-0.3594	-0.3533	3.3301	-0.6198	1.794	0.0209	0.2089	0.108	-0.3415	-0.0185	-0.1151	-0.0467	0.0646	-0.0035	0.1137	-0.0203	-0.0023	0.0951	0.0041	0.0845	38.9712	8.2089	7.5177
3	2.1673	1.1455	0.0846	1.611	0.1152	1.4138	0.0929	-0.2431	0.0162	0.2395	-0.1232	-0.0101	0.101	0.0055	0.0277	0.1437	-0.0101	-0.0043	0.0832	-0.0047	0.0877	30.5352	-1.6522	22.8769
4	2.6516	-0.363	0.4143	1.7409	0.0687	0.4668	-0.1432	0.0672	-0.1958	-0.059	0.2038	-0.2472	0.236	0.6717	-0.0542	0.1718	0.049	0.0172	0.4187	-0.0052	0.1624	82.2727	-11.9429	22.3774
5	0.8321	0.03	-0.3268	2.5623	-0.0569	1.2838	-0.0171	-0.1873	0.0735	0.2165	0.1005	-0.0283	-0.1421	0.1786	-0.0791	0.132	-0.0514	-0.0125	0.1792	-0.0094	0.0908	63.7238	9.7758	36.1198
6	1.0966	-1.0226	-0.169	1.5784	-0.2888	1.6279	-0.0229	-0.0174	0.009	-0.0675	0.0529	-0.0641	0.0769	0.2679	-0.0184	0.1031	-0.0644	-0.0142	0.2103	-0.0198	0.1242	71.9776	-2.7222	23.3586

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 4:79)	A	4 - 79
2	X-RAY DIFFRACTION	2	(chain A and resid 80:182)	A	80 - 182
3	X-RAY DIFFRACTION	3	(chain A and resid 183:361)	A	183 - 361
4	X-RAY DIFFRACTION	4	(chain B and resid 4:72)	B	4 - 72
5	X-RAY DIFFRACTION	5	(chain B and resid 73:182)	B	73 - 182
6	X-RAY DIFFRACTION	6	(chain B and resid 183:361)	B	183 - 361

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