PDB-6cd7: Crystal structure of APH(2")-IVa in complex with plazomicin

ID or keywords:

Entry

Database: PDB / ID: 6cd7

Title

Crystal structure of APH(2")-IVa in complex with plazomicin

Components

APH(2'')-Id

Keywords

TRANSFERASE/ANTIBIOTIC / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / AMINOGLYCOSIDE PHOSPHOTRANSFERASE / KINASE / TRANSFERASE / AMINOGLYCOSIDES / PLAZOMICIN / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX

Function / homology

Function and homology information

nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Enterococcus casseliflavus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.53 Å

Authors

Stogios, P.J. / Evdokimova, E. / Dong, A. / Di Leo, R. / Savchenko, A. / Satchell, K.J. / Joachimiak, J. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201200026C	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201700060C	United States

Citation

Journal: ACS Infect Dis / Year: 2018
Title: Plazomicin Retains Antibiotic Activity against Most Aminoglycoside Modifying Enzymes.
Authors: Cox, G. / Ejim, L. / Stogios, P.J. / Koteva, K. / Bordeleau, E. / Evdokimova, E. / Sieron, A.O. / Savchenko, A. / Serio, A.W. / Krause, K.M. / Wright, G.D.

History

Deposition	Feb 8, 2018	Deposition site: RCSB / Processing site: RCSB
Supersession	Feb 28, 2018	ID: 6C0C
Revision 1.0	Feb 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 25, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jun 20, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6cd7.cif.gz	293 KB	Display	PDBx/mmCIF format
PDB format	pdb6cd7.ent.gz	235 KB	Display	PDB format
PDBx/mmJSON format	6cd7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6cd7_validation.pdf.gz	726.8 KB	Display	wwPDB validaton report
Full document	6cd7_full_validation.pdf.gz	734.8 KB	Display
Data in XML	6cd7_validation.xml.gz	37 KB	Display
Data in CIF	6cd7_validation.cif.gz	59.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cd/6cd7 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/6cd7	HTTPS FTP

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Related structure data

Related structure data	5us1C 4dfbS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4de4-2 5c4k-1 4de4-1 5c4l-1 4dt8-1 4dt8-2 4dt9-1 4dfb-1 3sg9-2 4dta-2 3n4t-d 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
Other databases	TargetTrack: CSGID-IDP91189

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (2)

Deposited unit

A: APH(2'')-Id

B: APH(2'')-Id

hetero molecules

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

1

A: APH(2'')-Id

hetero molecules

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

2

B: APH(2'')-Id

hetero molecules

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

Unit cell

Length a, b, c (Å)	43.455, 101.813, 72.921
Angle α, β, γ (deg.)	90.00, 98.47, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	APH(2'')-Id Mass: 35482.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2'')-Id / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: O68183
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-EDS / (2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-4-{[(2S,3R)-3-amino-6-{[(2-hydroxyethyl)amino]methyl}-3,4-dihydro-2H-pyran-2-y l]oxy}-2-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]-2-hydroxybutanamide / plazomicin Mass: 592.683 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₅H₄₈N₆O₁₀ / Comment: antibiotic*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1155 / 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: 2.25 Å³/Da / Density % sol: 45.29 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M NACL, 10 MM HEPES (PH 7.5), 25% (W/V) PEG3350 AND 10 MM PLAZOMICIN

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
Detector	Type: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 10, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.53→19.6 Å / Num. obs: 93863 / % possible obs: 99.4 % / Redundancy: 3.9 % / CC_1/2: 1 / R_merge(I) obs: 0.032 / Net I/σ(I): 15.4
Reflection shell	Resolution: 1.53→1.56 Å / Redundancy: 3 % / R_merge(I) obs: 0.708 / Mean I/σ(I) obs: 1.3 / CC_1/2: 0.571 / % possible all: 93.5

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Processing

Software

Name	Version	Classification
PHENIX	dev_2733	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing
PHENIX		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4DFB

4dfb

Resolution: 1.53→19.597 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.22 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2084	4782	5.1 %	RANDOM
R_work	0.1709	-	-	-
obs	0.1728	93819	99.46 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.53→19.597 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4938	0	45	1155	6138

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5223
X-RAY DIFFRACTION	f_angle_d	1.09	7071
X-RAY DIFFRACTION	f_dihedral_angle_d	22.973	2023
X-RAY DIFFRACTION	f_chiral_restr	0.065	753
X-RAY DIFFRACTION	f_plane_restr	0.006	910

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 (%)
1.53-1.5474	0.3804	152	0.2895	2720	X-RAY DIFFRACTION	91
1.5474-1.5656	0.2787	136	0.2861	2930	X-RAY DIFFRACTION	99
1.5656-1.5847	0.2726	150	0.2629	2982	X-RAY DIFFRACTION	99
1.5847-1.6047	0.2686	150	0.2427	2973	X-RAY DIFFRACTION	99
1.6047-1.6258	0.2725	162	0.2382	2933	X-RAY DIFFRACTION	100
1.6258-1.6481	0.2739	159	0.2279	2956	X-RAY DIFFRACTION	100
1.6481-1.6716	0.2594	159	0.2223	2996	X-RAY DIFFRACTION	100
1.6716-1.6966	0.2194	180	0.2042	2946	X-RAY DIFFRACTION	100
1.6966-1.7231	0.2309	173	0.2024	2950	X-RAY DIFFRACTION	100
1.7231-1.7513	0.2576	144	0.2022	2938	X-RAY DIFFRACTION	100
1.7513-1.7815	0.218	138	0.2032	3026	X-RAY DIFFRACTION	100
1.7815-1.8138	0.2338	155	0.1964	3031	X-RAY DIFFRACTION	100
1.8138-1.8487	0.2378	162	0.1963	2903	X-RAY DIFFRACTION	100
1.8487-1.8864	0.2445	166	0.194	3021	X-RAY DIFFRACTION	100
1.8864-1.9274	0.2145	171	0.1979	2917	X-RAY DIFFRACTION	100
1.9274-1.9722	0.2058	170	0.1821	3001	X-RAY DIFFRACTION	100
1.9722-2.0214	0.2099	156	0.1789	2949	X-RAY DIFFRACTION	100
2.0214-2.076	0.2306	174	0.1787	2964	X-RAY DIFFRACTION	100
2.076-2.1371	0.232	152	0.1761	2992	X-RAY DIFFRACTION	100
2.1371-2.206	0.2241	174	0.1742	2973	X-RAY DIFFRACTION	100
2.206-2.2847	0.2415	169	0.1733	2970	X-RAY DIFFRACTION	100
2.2847-2.376	0.2248	151	0.1688	2969	X-RAY DIFFRACTION	100
2.376-2.4839	0.1982	156	0.1607	2978	X-RAY DIFFRACTION	100
2.4839-2.6146	0.2018	173	0.1621	2986	X-RAY DIFFRACTION	100
2.6146-2.778	0.2309	154	0.1711	2997	X-RAY DIFFRACTION	100
2.778-2.9918	0.193	166	0.162	2988	X-RAY DIFFRACTION	100
2.9918-3.2916	0.1809	150	0.1507	3008	X-RAY DIFFRACTION	100
3.2916-3.765	0.1937	159	0.1398	2993	X-RAY DIFFRACTION	100
3.765-4.7324	0.1507	150	0.1315	3016	X-RAY DIFFRACTION	100
4.7324-19.5982	0.1808	171	0.1632	3031	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	5.6892	1.055	-0.0271	4.9913	0.6089	6.4026	0.0462	0.0387	-0.0313	-0.0182	0.0161	0.7394	0.3267	-0.4862	-0.0481	0.1757	-0.0674	-0.0148	0.1738	0.0108	0.2532	40.2899	-23.2615	19.0605
2	1.2683	-0.1325	0.6797	0.6445	-0.5059	1.6311	-0.0096	0.0513	-0.024	-0.0463	-0.0323	-0.0279	0.0343	0.0484	0.0323	0.1277	0.0033	0.0236	0.0745	-0.0033	0.1138	56.828	-20.6236	27.8755
3	4.868	-3.3905	0.6028	4.8835	-0.4161	1.486	0.0463	0.0097	0.1911	0.0916	-0.0366	-0.3671	-0.0173	0.0112	-0.0069	0.25	-0.0699	0.0145	0.1151	-0.0005	0.2223	58.7132	8.4146	36.4136
4	2.4866	1.0943	0.316	3.5814	-0.152	2.4644	0.0234	-0.2277	0.0052	0.166	-0.0971	-0.0887	-0.1377	-0.072	0.0866	0.1269	0.0246	-0.002	0.0849	0.025	0.09	61.0982	-17.1077	40.8575
5	8.9346	-2.0133	3.1295	8.753	-3.9279	7.0602	0.0693	-0.0115	-0.0486	0.0821	0.3637	0.8409	0.3573	-0.7384	-0.4177	0.3277	-0.0913	0.0605	0.2217	0.0529	0.302	48.4215	1.1851	38.1987
6	2.4665	0.049	-0.2115	1.8358	0.0262	0.7724	0.0132	0.0523	0.0375	0.0069	-0.0385	0.1595	0.0454	-0.0537	0.02	0.1025	-0.0033	-0.0151	0.1035	-0.0207	0.0803	50.6841	11.1428	12.3072
7	1.2839	-0.0042	-0.2752	3.6821	-2.5603	4.0298	-0.0243	0.1887	0.115	-0.2263	-0.0229	-0.1253	-0.0094	-0.0157	0.0754	0.1152	-0.0175	0.0077	0.1404	0.0051	0.1037	68.6863	11.5673	-2.1242
8	7.2342	3.2718	3.5904	4.7765	2.5194	4.0181	0.112	0.0355	-0.2169	0.0376	0.1598	-0.2326	-0.093	-0.0104	-0.2255	0.2079	0.0121	0.0198	0.0995	-0.022	0.1963	61.7048	-19.2214	-1.9168
9	1.4117	-0.4578	-0.2713	2.9136	-0.8096	1.6317	0.0516	0.4473	0.0367	-0.4913	-0.1111	-0.1436	0.1169	-0.0526	0.0624	0.1882	-0.0154	0.0222	0.2152	0.0093	0.101	67.5765	7.2726	-4.448
10	8.8461	5.9253	-1.3159	5.3659	-2.1048	2.7944	0.0359	0.6344	0.0857	-0.404	0.2862	0.4147	-0.2845	-0.4748	-0.311	0.4225	0.08	0.0186	0.261	-0.0359	0.2232	55.9366	-10.1519	-6.4744

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 0:42)
2	X-RAY DIFFRACTION	2	(chain A and resid 43:145)
3	X-RAY DIFFRACTION	3	(chain A and resid 146:188)
4	X-RAY DIFFRACTION	4	(chain A and resid 189:264)
5	X-RAY DIFFRACTION	5	(chain A and resid 265:298)
6	X-RAY DIFFRACTION	6	(chain B and resid 0:98)
7	X-RAY DIFFRACTION	7	(chain B and resid 99:144)
8	X-RAY DIFFRACTION	8	(chain B and resid 145:188)
9	X-RAY DIFFRACTION	9	(chain B and resid 189:256)
10	X-RAY DIFFRACTION	10	(chain B and resid 257:297)

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