PDB-7cl5: The crystal structure of KanJ in complex with kanamycin B and N-o...

ID or keywords:

Entry

Database: PDB / ID: 7cl5

Title

The crystal structure of KanJ in complex with kanamycin B and N-oxalylglycine

Components

Kanamycin B dioxygenase

Keywords

OXIDOREDUCTASE / Dioxygenase / kanamycin biosynthesis

Function / homology

Function and homology information

kanamycin B dioxygenase / kanamycin biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity
Similarity search - Function

Biological species

Streptomyces kanamyceticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Kitayama, Y. / Miyanaga, A. / Kudo, F. / Eguchi, T.

Citation

Journal: Chembiochem / Year: 2021
Title: Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Authors: Kudo, F. / Kitayama, Y. / Miyanaga, A. / Numakura, M. / Eguchi, T.

History

Deposition	Jul 20, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 13, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 20, 2021	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	May 12, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3	Nov 29, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7cl5.cif.gz	681.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7cl5.ent.gz	564.3 KB	Display	PDB format
PDBx/mmJSON format	7cl5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7cl5_validation.pdf.gz	5.8 MB	Display	wwPDB validaton report
Full document	7cl5_full_validation.pdf.gz	5.8 MB	Display
Data in XML	7cl5_validation.xml.gz	58.4 KB	Display
Data in CIF	7cl5_validation.cif.gz	78.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cl/7cl5 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/7cl5	HTTPS FTP

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Related structure data

Related structure data	7cl2SC 7cl3C 7cl4C 7cl6C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7cl3-1 7cl4-1 7cl6-3 7cl3-3 7cl2-3 7cl6-1 7cl2-2 7cl6-2 7cl2-1 7cl3-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

7cl2SC

7cl3C

7cl4C

7cl6C

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	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (1)

Deposited unit

A: Kanamycin B dioxygenase

B: Kanamycin B dioxygenase

C: Kanamycin B dioxygenase

D: Kanamycin B dioxygenase

E: Kanamycin B dioxygenase

F: Kanamycin B dioxygenase

hetero molecules

206 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Kanamycin B dioxygenase

B: Kanamycin B dioxygenase

hetero molecules

defined by author
Evidence: gel filtration
68.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Kanamycin B dioxygenase

hetero molecules

D: Kanamycin B dioxygenase

hetero molecules

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

3

E: Kanamycin B dioxygenase

F: Kanamycin B dioxygenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.083, 184.259, 109.771
Angle α, β, γ (deg.)	90.000, 97.680, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	ALA	ALA	A	A	2 - 283	18 - 299
2	1	ALA	ALA	ALA	ALA	B	B	2 - 283	18 - 299
1	2	HIS	HIS	VAL	VAL	A	A	0 - 284	16 - 300
2	2	HIS	HIS	VAL	VAL	C	C	0 - 284	16 - 300
1	3	HIS	HIS	VAL	VAL	A	A	0 - 284	16 - 300
2	3	HIS	HIS	VAL	VAL	D	D	0 - 284	16 - 300
1	4	LEU	LEU	ALA	ALA	A	A	3 - 283	19 - 299
2	4	LEU	LEU	ALA	ALA	E	E	3 - 283	19 - 299
1	5	HIS	HIS	VAL	VAL	A	A	0 - 284	16 - 300
2	5	HIS	HIS	VAL	VAL	F	F	0 - 284	16 - 300
1	6	ALA	ALA	ALA	ALA	B	B	2 - 283	18 - 299
2	6	ALA	ALA	ALA	ALA	C	C	2 - 283	18 - 299
1	7	ALA	ALA	ALA	ALA	B	B	2 - 283	18 - 299
2	7	ALA	ALA	ALA	ALA	D	D	2 - 283	18 - 299
1	8	LEU	LEU	ALA	ALA	B	B	3 - 283	19 - 299
2	8	LEU	LEU	ALA	ALA	E	E	3 - 283	19 - 299
1	9	ALA	ALA	VAL	VAL	B	B	2 - 284	18 - 300
2	9	ALA	ALA	VAL	VAL	F	F	2 - 284	18 - 300
1	10	HIS	HIS	VAL	VAL	C	C	0 - 284	16 - 300
2	10	HIS	HIS	VAL	VAL	D	D	0 - 284	16 - 300
1	11	LEU	LEU	ALA	ALA	C	C	3 - 283	19 - 299
2	11	LEU	LEU	ALA	ALA	E	E	3 - 283	19 - 299
1	12	HIS	HIS	VAL	VAL	C	C	0 - 284	16 - 300
2	12	HIS	HIS	VAL	VAL	F	F	0 - 284	16 - 300
1	13	LEU	LEU	ALA	ALA	D	D	3 - 283	19 - 299
2	13	LEU	LEU	ALA	ALA	E	E	3 - 283	19 - 299
1	14	HIS	HIS	VAL	VAL	D	D	0 - 284	16 - 300
2	14	HIS	HIS	VAL	VAL	F	F	0 - 284	16 - 300
1	15	LEU	LEU	VAL	VAL	E	E	3 - 284	19 - 300
2	15	LEU	LEU	VAL	VAL	F	F	3 - 284	19 - 300

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Kanamycin B dioxygenase / Kanamycin biosynthesis protein J Mass: 33604.117 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces kanamyceticus (bacteria) / Gene: kanJ, kacB / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / References: UniProt: Q6L732, kanamycin B dioxygenase
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-OGA / N-OXALYLGLYCINE Mass: 147.086 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₅NO₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-9CS / (1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE / Kanamycin B / Bekanamycin Mass: 483.514 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₈H₃₇N₅O₁₀ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.49 Å³/Da / Density % sol: 50.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000, Lithium sulfate, Tris

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 26, 2019
Radiation	Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 67780 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC_1/2: 0.997 / R_merge(I) obs: 0.06 / R_pim(I) all: 0.057 / R_rim(I) all: 0.083 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.5→2.56 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.597 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4519 / CC_1/2: 0.629 / R_pim(I) all: 0.564 / R_rim(I) all: 0.823 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7CL2

7cl2

Resolution: 2.5→49.68 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.939 / SU B: 21.136 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.584 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2143	3327	4.9 %	RANDOM
R_work	0.1966	-	-	-
obs	0.1975	64414	99.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 136.23 Å² / B_iso mean: 58.121 Å² / B_iso min: 23.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.74 Å²	0 Å²	0.71 Å²
2-	-	-0.61 Å²	0 Å²
3-	-	-	2.08 Å²

Refinement step

Cycle: final / Resolution: 2.5→49.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13159	0	264	182	13605
B_iso mean	-	-	45.15	44.75	-
Num. residues	-	-	-	-	1685

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	13834
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	12524
X-RAY DIFFRACTION	r_angle_refined_deg	1.386	1.668	19039
X-RAY DIFFRACTION	r_angle_other_deg	1.17	1.584	29142
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.369	5	1673
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.265	21.317	729
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.063	15	1963
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.231	15	102
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1817
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	15293
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2717

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	8929	0.04
1	2	B	8929	0.04
2	1	A	9126	0.04
2	2	C	9126	0.04
3	1	A	9127	0.04
3	2	D	9127	0.04
4	1	A	8908	0.04
4	2	E	8908	0.04
5	1	A	8979	0.04
5	2	F	8979	0.04
6	1	B	8902	0.05
6	2	C	8902	0.05
7	1	B	8930	0.04
7	2	D	8930	0.04
8	1	B	8911	0.04
8	2	E	8911	0.04
9	1	B	8851	0.04
9	2	F	8851	0.04
10	1	C	9094	0.04
10	2	D	9094	0.04
11	1	C	8898	0.05
11	2	E	8898	0.05
12	1	C	8969	0.05
12	2	F	8969	0.05
13	1	D	8907	0.05
13	2	E	8907	0.05
14	1	D	8996	0.04
14	2	F	8996	0.04
15	1	E	8858	0.04
15	2	F	8858	0.04

LS refinement shell

Resolution: 2.5→2.565 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.316	221	-
R_work	0.317	4747	-
all	-	4968	-
obs	-	-	99.96 %

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	2.5064	-1.277	0.6264	2.8482	-0.8823	2.0668	0.1769	-0.0239	-0.2661	-0.3082	0.0995	0.1161	0.4301	-0.0591	-0.2764	0.2985	-0.0341	-0.022	0.1753	0.0106	0.061	-18.808	49.716	92.235
2	1.1915	-0.1943	-0.4027	1.5373	-0.0753	0.9616	0.1132	0.056	-0.1317	-0.0381	0.0402	0.0184	-0.2586	0.1198	-0.1533	0.4677	-0.0688	0.0588	0.3907	-0.0322	0.0639	-33.267	83.428	78.39
3	1.8992	-0.2122	0.0118	1.3589	0.0658	2.6895	-0.0947	0.1448	-0.0223	0.2491	0.034	-0.1225	0.1507	-0.1005	0.0607	0.3981	0.0044	0.0576	0.3125	-0.0323	0.0323	-12.402	7.819	-4.971
4	1.4799	0.0261	-0.0464	1.188	0.5853	3.4581	0.1374	-0.0939	0.1702	-0.2049	-0.1883	0.0829	-0.1464	-0.3389	0.0508	0.3221	0.0619	0.0378	0.3555	-0.0287	0.0301	25.986	13.378	-41.97
5	1.6463	0.2385	-0.3103	2.4417	1.2948	2.7027	0.0317	0.0628	-0.061	0.7324	0.1597	-0.3511	0.449	0.2061	-0.1914	0.5786	0.2046	-0.2376	0.359	-0.1337	0.1102	9.928	33.809	21.63
6	1.2573	-0.0921	-0.6079	2.3017	1.9879	3.9961	0.0337	0.0759	-0.1635	-0.7347	-0.3962	0.4774	-0.822	-0.2931	0.3624	0.6151	0.1738	-0.2799	0.332	-0.1725	0.1872	0.829	66.723	41.045

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 284
2	X-RAY DIFFRACTION	1	A	301 - 303
3	X-RAY DIFFRACTION	2	B	2 - 284
4	X-RAY DIFFRACTION	2	B	301 - 303
5	X-RAY DIFFRACTION	3	C	0 - 284
6	X-RAY DIFFRACTION	3	C	301 - 303
7	X-RAY DIFFRACTION	4	D	0 - 284
8	X-RAY DIFFRACTION	4	D	301 - 303
9	X-RAY DIFFRACTION	5	E	3 - 284
10	X-RAY DIFFRACTION	5	E	301 - 303
11	X-RAY DIFFRACTION	6	F	0 - 284
12	X-RAY DIFFRACTION	6	F	301 - 303

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