PDB-6qwd: Crystal structure of KPC-3

ID or keywords:

Entry

Database: PDB / ID: 6qwd

Title

Crystal structure of KPC-3

Components

Beta-lactamase

Keywords

ANTIMICROBIAL PROTEIN / antibiotic resistance / serine beta-lactamase

Function / homology

Function and homology information

beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.2 Å

Authors

Tooke, C.L. / Hinchliffe, P. / Spencer, J.

Funding support

United Kingdom, 1items

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2019
Title: Molecular Basis of Class A beta-Lactamase Inhibition by Relebactam.
Authors: Tooke, C.L. / Hinchliffe, P. / Lang, P.A. / Mulholland, A.J. / Brem, J. / Schofield, C.J. / Spencer, J.

History

Deposition	Mar 5, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 21, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6qwd.cif.gz	181.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6qwd.ent.gz	147 KB	Display	PDB format
PDBx/mmJSON format	6qwd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6qwd_validation.pdf.gz	444.9 KB	Display	wwPDB validaton report
Full document	6qwd_full_validation.pdf.gz	444.6 KB	Display
Data in XML	6qwd_validation.xml.gz	14.9 KB	Display
Data in CIF	6qwd_validation.cif.gz	22.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qw/6qwd ftp://data.pdbj.org/pub/pdb/validation_reports/qw/6qwd	HTTPS FTP

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Related structure data

Related structure data	6qw7C 6qw8C 6qw9C 6qwaC 6qwbC 6qwcC 6qweC 5ul8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5oyo-1 1rjk-d 6cyn-5 4c3q-d 3w4p-d 1bza-d 1rhr-d 3lum-1 6h2g-2 5eec-1 Search similar-shape structures by Omokage search (details) 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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #164 - Aug 2013 Serotonin Receptor similarity (3) #29 - May 2002 Penicillin-binding Proteins similarity (1)

Deposited unit

A: Beta-lactamase

hetero molecules

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

1

Idetical with deposited unit
defined by software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	60.006, 78.624, 56.008
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-305- SO4
2	1	A-481- HOH

#1: Protein	Beta-lactamase Mass: 30831.658 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: pUCLAKPC1_410 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: A0A220QIS6, UniProt: Q9F663*PLUS, beta-lactamase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.59 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M Ammonium sulphate, 5% ethanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.78 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 4, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.78 Å / Relative weight: 1
Reflection	Resolution: 1.2→32.88 Å / Num. obs: 83425 / % possible obs: 100 % / Redundancy: 12.7 % / R_pim(I) all: 0.047 / Net I/σ(I): 10.8
Reflection shell	Resolution: 1.2→1.22 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4118 / R_pim(I) all: 0.566

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5UL8

5ul8

Resolution: 1.2→32.177 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.44

	R_factor	Num. reflection	% reflection
R_free	0.1579	4198	5.03 %
R_work	0.143	-	-
obs	0.1437	83425	99.94 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.2→32.177 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2001	0	37	306	2344

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2251
X-RAY DIFFRACTION	f_angle_d	1.007	3091
X-RAY DIFFRACTION	f_dihedral_angle_d	12.701	816
X-RAY DIFFRACTION	f_chiral_restr	0.077	339
X-RAY DIFFRACTION	f_plane_restr	0.008	408

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 (%)
1.2-1.2136	0.2695	135	0.2503	2633	X-RAY DIFFRACTION	100
1.2136-1.2279	0.2604	129	0.2477	2611	X-RAY DIFFRACTION	100
1.2279-1.2429	0.2401	145	0.239	2597	X-RAY DIFFRACTION	100
1.2429-1.2586	0.2772	134	0.2305	2597	X-RAY DIFFRACTION	100
1.2586-1.2752	0.218	123	0.2268	2652	X-RAY DIFFRACTION	100
1.2752-1.2927	0.2417	138	0.2197	2613	X-RAY DIFFRACTION	100
1.2927-1.3111	0.2113	144	0.2077	2586	X-RAY DIFFRACTION	100
1.3111-1.3307	0.2029	143	0.1972	2607	X-RAY DIFFRACTION	100
1.3307-1.3515	0.2059	143	0.1957	2610	X-RAY DIFFRACTION	100
1.3515-1.3736	0.193	137	0.1881	2622	X-RAY DIFFRACTION	100
1.3736-1.3973	0.2038	145	0.1873	2619	X-RAY DIFFRACTION	100
1.3973-1.4227	0.1918	123	0.1749	2611	X-RAY DIFFRACTION	100
1.4227-1.4501	0.1941	134	0.1674	2616	X-RAY DIFFRACTION	100
1.4501-1.4797	0.1545	162	0.1537	2610	X-RAY DIFFRACTION	100
1.4797-1.5119	0.1626	149	0.1491	2621	X-RAY DIFFRACTION	100
1.5119-1.547	0.1602	133	0.1456	2623	X-RAY DIFFRACTION	100
1.547-1.5857	0.1538	127	0.1444	2630	X-RAY DIFFRACTION	100
1.5857-1.6286	0.1753	141	0.1403	2619	X-RAY DIFFRACTION	100
1.6286-1.6765	0.1635	143	0.1326	2649	X-RAY DIFFRACTION	100
1.6765-1.7306	0.1651	132	0.1315	2630	X-RAY DIFFRACTION	100
1.7306-1.7925	0.1439	160	0.1295	2616	X-RAY DIFFRACTION	100
1.7925-1.8643	0.1388	126	0.1279	2676	X-RAY DIFFRACTION	100
1.8643-1.9491	0.1354	126	0.1229	2654	X-RAY DIFFRACTION	100
1.9491-2.0518	0.1281	140	0.1145	2650	X-RAY DIFFRACTION	100
2.0518-2.1804	0.1179	144	0.1142	2646	X-RAY DIFFRACTION	100
2.1804-2.3487	0.1193	165	0.1134	2663	X-RAY DIFFRACTION	100
2.3487-2.5849	0.1428	143	0.1162	2678	X-RAY DIFFRACTION	100
2.5849-2.9587	0.1477	155	0.1201	2678	X-RAY DIFFRACTION	100
2.9587-3.7268	0.1427	140	0.1274	2747	X-RAY DIFFRACTION	100
3.7268-32.1885	0.162	139	0.1499	2863	X-RAY DIFFRACTION	100

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	3.6784	0.7993	-0.4891	7.5091	-3.9882	6.2378	-0.0331	0.4035	-0.0062	-0.6158	-0.0383	-0.0573	0.1491	0.1508	0.0857	0.1452	-0.0061	0.0049	0.1834	-0.0364	0.1152	11.5523	10.2081	-4.2769
2	2.3382	1.0519	-0.7418	1.8719	-0.6508	2.2278	-0.007	0.214	0.15	-0.0714	-0.0029	0.0287	-0.1048	-0.0142	-0.0021	0.0603	0.0046	-0.0094	0.0873	0.0147	0.0686	8.8129	18.1671	2.4762
3	1.7342	0.3499	1.3582	2.5371	-0.6942	3.4053	-0.177	-0.1801	0.2302	0.1595	0.0186	0.0374	-0.5608	-0.0439	0.1317	0.0983	0.0066	0.0006	0.1186	-0.0378	0.1049	14.3439	26.9826	28.2751
4	3.3694	0.4208	1.2947	2.2044	-0.3374	4.5966	0.0779	-0.0328	-0.176	0.032	-0.002	0.0028	0.1935	0.0641	-0.0828	0.0664	-0.0039	-0.0106	0.1246	-0.0053	0.0816	20.2489	15.3786	31.4556
5	5.0648	-3.8006	2.9157	3.5315	-2.6917	2.5924	-0.1366	-0.2771	0.1815	0.1567	0.0761	-0.0957	-0.1362	-0.0832	0.0779	0.1001	-0.0111	-0.0022	0.1019	-0.0291	0.1004	7.1674	23.4633	25.8829
6	1.2198	0.1772	-0.1432	0.5398	-0.0843	0.6305	0.0179	-0.0325	0.0732	0.01	-0.0219	-0.0417	-0.0499	0.051	0.0031	0.068	-0.01	-0.0007	0.0729	-0.0005	0.0667	13.9559	19.6231	14.1574
7	4.7663	5.0056	-2.1812	8.0802	-2.9945	1.4687	-0.0616	0.1014	-0.0126	-0.1051	0.0595	0.027	0.0512	-0.0043	-0.006	0.062	-0.0057	-0.0096	0.0795	-0.0074	0.0173	13.2568	11.6129	7.4598
8	0.9576	2.1689	-2.203	6.446	-5.4604	5.5847	-0.0911	0.0745	-0.0454	-0.1932	-0.1352	-0.4155	0.0896	0.2545	0.2652	0.0881	0.0011	0.0226	0.1404	0.0012	0.1196	20.2832	14.1494	-0.4711

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 41 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 42 through 68 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 98 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 99 through 131 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 132 through 155 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 156 through 251 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 252 through 275 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 276 through 294 )

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