PDB-6cyk: CTX-M-14 N106S mutant

ID or keywords:

Entry

Database: PDB / ID: 6cyk

Title

CTX-M-14 N106S mutant

Components

Beta-lactamase

Keywords

HYDROLASE / Beta-lactamase CTX-M-14

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Patel, M.P. / Hu, L. / Sankaran, B. / Brown, C. / Prasad, B.V.V. / Palzkill, T.

Funding support

United States, 1items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Synergistic effects of functionally distinct substitutions in beta-lactamase variants shed light on the evolution of bacterial drug resistance.
Authors: Patel, M.P. / Hu, L. / Brown, C.A. / Sun, Z. / Adamski, C.J. / Stojanoski, V. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.

History

Deposition	Apr 6, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 10, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 17, 2018	Group: Data collection / Database references / Structure summary Category: citation / citation_author / entity Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2	Nov 28, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jun 30, 2021	Group: Structure summary / Category: audit_author
Revision 1.5	Oct 4, 2023	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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6cyk.cif.gz	222.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6cyk.ent.gz	175.4 KB	Display	PDB format
PDBx/mmJSON format	6cyk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6cyk_validation.pdf.gz	439.3 KB	Display	wwPDB validaton report
Full document	6cyk_full_validation.pdf.gz	440.7 KB	Display
Data in XML	6cyk_validation.xml.gz	27.7 KB	Display
Data in CIF	6cyk_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cy/6cyk ftp://data.pdbj.org/pub/pdb/validation_reports/cy/6cyk	HTTPS FTP

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Related structure data

Related structure data	6cynC 6cyqC 6cyuC 4pm5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3bfd-2 4pm7-d 5mgi-d 3bff-2 3bfd-4 3c5a-d 6jn3-2 6b1f-2 1yms-1 4de1-1 6d7h-d 6ook-1 3g32-2 4zbe-d 6cyn-2 4dds-2 4pma-d 3bfc-3 6qwc-d 3bff-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

S: Starting model for refinement

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	#164 - Aug 2013 Serotonin Receptor similarity (5) #29 - May 2002 Penicillin-binding Proteins similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.210, 107.160, 47.800
Angle α, β, γ (deg.)	90.00, 101.72, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase Mass: 27973.520 Da / Num. of mol.: 2 / Mutation: N106S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, APT94_14605, BET08_34355, BJJ90_27545, ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, APT94_14605, BET08_34355, BJJ90_27545, BK334_27290, BMR21_24310, BMR35_25520, BMR49_25760, BXT93_06855, CA268_29135, CDL37_21060, CR538_26855, ETN48_p0088, pCT_085, pHK01_011 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9L5C7, UniProt: Q9L5C8*PLUS, beta-lactamase
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 763 / 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: 2.03 Å³/Da / Density % sol: 39.3 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.2 M calcium acetate hydrate, 20% (w/v) PEG 3350, pH 7.5

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1 Å
Detector	Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 2, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.7→23.4 Å / Num. obs: 96247 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC_1/2: 0.993 / R_merge(I) obs: 0.091 / Net I/σ(I): 8.8
Reflection shell	Resolution: 1.7→1.73 Å / R_merge(I) obs: 0.516 / CC_1/2: 0.721

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4PM5

4pm5

Resolution: 1.7→22.92 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 17.41

	R_factor	Num. reflection	% reflection
R_free	0.1852	4816	5 %
R_work	0.1512	-	-
obs	0.1529	96247	99.62 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→22.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3902	0	8	765	4675

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4036
X-RAY DIFFRACTION	f_angle_d	0.853	5505
X-RAY DIFFRACTION	f_dihedral_angle_d	6.834	3339
X-RAY DIFFRACTION	f_chiral_restr	0.054	653
X-RAY DIFFRACTION	f_plane_restr	0.006	727

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 (%)
1.7-1.7193	0.2858	187	0.2613	2973	X-RAY DIFFRACTION	99
1.7193-1.7395	0.2974	185	0.2543	2956	X-RAY DIFFRACTION	97
1.7395-1.7607	0.2957	204	0.2436	2965	X-RAY DIFFRACTION	100
1.7607-1.783	0.2891	150	0.2301	3060	X-RAY DIFFRACTION	99
1.783-1.8065	0.2124	158	0.2204	3006	X-RAY DIFFRACTION	98
1.8065-1.8312	0.2372	163	0.2086	3052	X-RAY DIFFRACTION	100
1.8312-1.8573	0.2508	162	0.2075	2999	X-RAY DIFFRACTION	99
1.8573-1.8851	0.2366	142	0.206	3083	X-RAY DIFFRACTION	99
1.8851-1.9145	0.2319	162	0.1963	3067	X-RAY DIFFRACTION	100
1.9145-1.9459	0.2411	176	0.1813	3038	X-RAY DIFFRACTION	100
1.9459-1.9794	0.2229	142	0.1736	3054	X-RAY DIFFRACTION	99
1.9794-2.0154	0.2036	168	0.1616	3047	X-RAY DIFFRACTION	100
2.0154-2.0541	0.1875	170	0.1531	3072	X-RAY DIFFRACTION	100
2.0541-2.096	0.1885	191	0.1498	2999	X-RAY DIFFRACTION	100
2.096-2.1416	0.1839	132	0.1492	3096	X-RAY DIFFRACTION	100
2.1416-2.1913	0.1814	183	0.1478	3051	X-RAY DIFFRACTION	100
2.1913-2.2461	0.1564	145	0.1432	3057	X-RAY DIFFRACTION	100
2.2461-2.3068	0.1811	159	0.1446	3046	X-RAY DIFFRACTION	100
2.3068-2.3746	0.177	187	0.1471	3058	X-RAY DIFFRACTION	100
2.3746-2.4511	0.1865	148	0.1394	3041	X-RAY DIFFRACTION	100
2.4511-2.5386	0.2062	151	0.1399	3103	X-RAY DIFFRACTION	100
2.5386-2.6402	0.1924	161	0.1418	3059	X-RAY DIFFRACTION	100
2.6402-2.7601	0.181	146	0.1415	3034	X-RAY DIFFRACTION	100
2.7601-2.9054	0.1838	136	0.1359	3085	X-RAY DIFFRACTION	100
2.9054-3.087	0.1644	167	0.1262	3059	X-RAY DIFFRACTION	100
3.087-3.3247	0.1472	141	0.1291	3084	X-RAY DIFFRACTION	100
3.3247-3.6581	0.1382	122	0.1137	3113	X-RAY DIFFRACTION	100
3.6581-4.1846	0.1261	166	0.1142	3055	X-RAY DIFFRACTION	100
4.1846-5.2616	0.1403	173	0.1261	3039	X-RAY DIFFRACTION	100
5.2616-22.9217	0.1671	139	0.1511	3080	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	1.6473	-0.5837	0.7103	1.1832	0.1011	2.3671	-0.0032	0.1052	0.1212	-0.0814	-0.0149	-0.153	-0.1568	0.1312	0.0093	0.1051	-0.0165	0.0141	0.0675	0.0096	0.1051	-5.7429	-5.3236	-17.2538
2	1.3937	0.6232	0.2172	1.8312	0.1409	1.1653	0.0172	-0.0241	-0.0321	0.001	-0.0036	0.0544	0.0565	-0.0842	-0.0129	0.071	-0.0004	0.0071	0.0699	0.0014	0.0637	-22.5301	-19.0477	4.0157
3	0.5182	-0.0043	0.0657	0.4499	0.0752	0.8192	0.0184	-0.0238	-0.0135	0.0208	0.0039	-0.0191	0.0014	0.0282	-0.0175	0.0853	-0.0009	0.0055	0.077	0.0005	0.0887	-12.3654	-13.3779	-5.6817
4	3.3833	-0.6631	1.6796	1.064	-0.1567	2.3095	0.0051	0.1287	-0.11	-0.0379	0.0181	-0.0363	0.0611	0.0701	-0.0198	0.0816	-0.0074	0.0183	0.039	0.0075	0.0596	-8.5919	-14.3668	-17.3354
5	0.3329	0.1571	0.0155	0.6017	-0.1974	1.917	-0.0437	0.048	0.0113	-0.1073	-0.0015	0.0315	-0.0285	-0.0544	0.0497	0.0797	0.0019	-0.001	0.0553	-0.008	0.0827	-14.873	-44.5937	-21.0468
6	3.8238	4.2073	-0.8885	4.8717	-1.5408	1.5208	0.1694	-0.2374	-0.2978	0.3485	-0.2956	-0.2446	-0.0677	0.2091	0.0589	0.1241	-0.0019	-0.0137	0.1158	-0.0009	0.0983	0.9885	-44.4164	5.2194
7	3.9339	0.4107	0.555	1.9088	0.2356	0.9648	0.02	0.0153	0.1582	-0.0679	-0.0925	-0.0693	-0.1579	0.0933	0.0673	0.1073	-0.0182	0.0011	0.075	-0.01	0.0817	0.776	-35.3049	-2.0459
8	0.2842	0.0448	0.1252	0.45	-0.0574	0.919	-0.0112	-0.0104	0.0007	-0.0068	0.0219	0.0217	0.0276	0.0026	-0.0106	0.0842	-0.0016	-0.0004	0.0786	-0.0098	0.084	-10.0167	-44.0097	-12.6492
9	6.456	0.4525	-3.6575	1.4959	-0.4829	3.3333	0.0041	-0.0702	0.1782	-0.1068	0.0154	0.0578	-0.0202	0.0869	-0.0096	0.0877	-0.0157	-0.0374	0.073	0.0028	0.0634	-12.8157	-37.0735	-22.5863
10	7.3618	1.4456	-1.48	4.9126	-0.5797	4.42	-0.0871	0.1489	0.1941	-0.1165	0.0806	0.3271	-0.1281	-0.3461	0.045	0.1076	0.0358	-0.0137	0.0767	-0.0022	0.073	-19.847	-33.2959	-25.0359

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 25 through 68 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 154 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 155 through 251 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 252 through 290 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 28 through 86 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 87 through 101 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 102 through 129 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 130 through 251 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 252 through 275 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 276 through 290 )

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