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- PDB-7cl3: The crystal structure of KanJ in complex with kanamycin B -

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Basic information

Entry
Database: PDB / ID: 7cl3
TitleThe crystal structure of KanJ in complex with kanamycin B
ComponentsKanamycin B dioxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase / kanamycin biosynthesis
Function / homology
Function and homology information


kanamycin B dioxygenase / kanamycin biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity
Similarity search - Function
: / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-9CS / NICKEL (II) ION / Kanamycin B dioxygenase
Similarity search - Component
Biological speciesStreptomyces kanamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKitayama, Y. / Miyanaga, A. / Kudo, F. / Eguchi, T.
CitationJournal: 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
DepositionJul 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 12, 2021Group: 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 1.3Nov 29, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)205,45424
Polymers201,6256
Non-polymers3,83018
Water6,630368
1
A: Kanamycin B dioxygenase
B: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4858
Polymers67,2082
Non-polymers1,2776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Kanamycin B dioxygenase
hetero molecules

D: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4858
Polymers67,2082
Non-polymers1,2776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
3
E: Kanamycin B dioxygenase
F: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4858
Polymers67,2082
Non-polymers1,2776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.289, 184.514, 109.543
Angle α, β, γ (deg.)90.000, 93.990, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPROAA2 - 28118 - 297
21ALAALAPROPROBB2 - 28118 - 297
12HISHISVALVALAA0 - 28416 - 300
22HISHISVALVALCC0 - 28416 - 300
13HISHISLEULEUAA0 - 27616 - 292
23HISHISLEULEUDD0 - 27616 - 292
14HISHISVALVALAA0 - 28416 - 300
24HISHISVALVALEE0 - 28416 - 300
15HISHISVALVALAA0 - 28416 - 300
25HISHISVALVALFF0 - 28416 - 300
16ALAALAGLYGLYBB2 - 27818 - 294
26ALAALAALAALACC2 - 28318 - 299
17ALAALALEULEUBB2 - 27618 - 292
27ALAALALEULEUDD2 - 27618 - 292
18ALAALAPROPROBB2 - 28118 - 297
28ALAALAPROPROEE2 - 28118 - 297
19ALAALAGLYGLYBB2 - 27818 - 294
29ALAALAALAALAFF2 - 28318 - 299
110HISHISPROPROCC0 - 28116 - 297
210HISHISLEULEUDD0 - 27616 - 292
111HISHISVALVALCC0 - 28416 - 300
211HISHISVALVALEE0 - 28416 - 300
112HISHISVALVALCC0 - 28416 - 300
212HISHISVALVALFF0 - 28416 - 300
113HISHISLEULEUDD0 - 27616 - 292
213HISHISLEULEUEE0 - 27616 - 292
114HISHISLEULEUDD0 - 27616 - 292
214HISHISPROPROFF0 - 28116 - 297
115HISHISVALVALEE0 - 28416 - 300
215HISHISVALVALFF0 - 28416 - 300

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

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Components

#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 BL21(DE3) (bacteria) / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / 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 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000, Lithium sulfate, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 26, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 100173 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.037 / Rrim(I) all: 0.054 / Net I/σ(I): 15.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4932 / CC1/2: 0.734 / Rpim(I) all: 0.455 / Rrim(I) all: 0.677 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CL2

7cl2


Resolution: 2.2→47.06 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 13.003 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 4908 4.9 %RANDOM
Rwork0.1944 ---
obs0.1955 95217 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.64 Å2 / Biso mean: 55.033 Å2 / Biso min: 28.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20.31 Å2
2--0.96 Å20 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 2.2→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13130 0 234 368 13732
Biso mean--61.62 47.09 -
Num. residues----1682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01313774
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712470
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.66818969
X-RAY DIFFRACTIONr_angle_other_deg1.2341.58429020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.29451672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89821.51715
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.598151962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.51515102
X-RAY DIFFRACTIONr_chiral_restr0.0660.21815
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022704
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87580.06
12B87580.06
21A89580.04
22C89580.04
31A89060.04
32D89060.04
41A89450.05
42E89450.05
51A89030.05
52F89030.05
61B87010.07
62C87010.07
71B87670.05
72D87670.05
81B87750.07
82E87750.07
91B86360.06
92F86360.06
101C88320.05
102D88320.05
111C88510.06
112E88510.06
121C88990.05
122F88990.05
131D88080.06
132E88080.06
141D88000.05
142F88000.05
151E88480.05
152F88480.05
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 382 -
Rwork0.279 7024 -
all-7406 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.1534-0.14570.1880.9359-0.09741.26210.04610.0381-0.0904-0.06860.12060.02390.12680.0438-0.16670.1240.007-0.01360.1336-0.05550.072-12.66849.83292.77
20.8967-0.41690.01751.59130.2590.76570.13770.0148-0.0073-0.2072-0.0485-0.1096-0.09210.0352-0.08920.1689-0.00990.05740.1751-0.00210.0286-27.50483.30978.589
31.0598-0.17590.64110.7955-0.05212.5088-0.11310.12680.0010.1199-0.039-0.08030.12890.10590.15210.17610.04180.01990.20050.00880.0221-12.8478.263-4.959
41.00580.0395-0.17651.0153-0.36532.35680.0666-0.00550.1168-0.1483-0.04880.00920.0946-0.1277-0.01780.18470.01680.02310.1749-0.00650.015523.24213.419-41.594
50.96020.8670.50921.38570.74111.8980.19580.1574-0.19590.50680.193-0.36570.35710.3326-0.38870.35840.2006-0.22390.251-0.15550.162310.98833.94520.709
60.5720.1791-0.66751.43572.01035.70470.15270.0014-0.0013-0.35180.1305-0.0045-0.78930.1893-0.28320.28260.0669-0.08950.1694-0.10540.13475.07666.50842.211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 303
2X-RAY DIFFRACTION2B2 - 303
3X-RAY DIFFRACTION3C0 - 303
4X-RAY DIFFRACTION4D0 - 303
5X-RAY DIFFRACTION5E0 - 303
6X-RAY DIFFRACTION6F0 - 303

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