[English] 日本語
Yorodumi
- PDB-6s0w: The crystal structure of kanamycin B dioxygenase (KanJ) from Stre... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s0w
TitleThe crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel and kanamycin B sulfate
ComponentsKanamycin B dioxygenase
KeywordsMETAL BINDING PROTEIN / non-heme iron dioxygenase / alpha-ketoglutarate dioxygenase / Kanamycin biosynthesis / KanJ / OXIDOREDUCTASE / kanamycin B
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)
Similarity search - Domain/homology
Chem-9CS / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Kanamycin B dioxygenase
Similarity search - Component
Biological speciesStreptomyces kanamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.36 Å
AuthorsMrugala, B. / Niedzialkowska, E. / Minor, W. / Borowski, T.
Funding support Poland, United States, 2items
OrganizationGrant numberCountry
Polish National Science Centre2014/15/B/NZ1/03331 Poland
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01-GM117325-01 United States
CitationJournal: Febs J. / Year: 2021
Title: A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates.
Authors: Mrugala, B. / Milaczewska, A. / Porebski, P.J. / Niedzialkowska, E. / Guzik, M. / Minor, W. / Borowski, T.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.title / _citation_author.identifier_ORCID ..._citation.title / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)196,23138
Polymers191,0476
Non-polymers5,18532
Water18,1411007
1
A: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5755
Polymers31,8411
Non-polymers7344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6716
Polymers31,8411
Non-polymers8305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6716
Polymers31,8411
Non-polymers8305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7787
Polymers31,8411
Non-polymers9376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6716
Polymers31,8411
Non-polymers8305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8648
Polymers31,8411
Non-polymers1,0237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.444, 186.061, 110.168
Angle α, β, γ (deg.)90.00, 95.20, 90.00
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
11LEULEULEULEUAA3 - 2766 - 279
21LEULEULEULEUBB3 - 2766 - 279
12LEULEULEULEUAA3 - 2766 - 279
22LEULEULEULEUCC3 - 2766 - 279
13LEULEULEULEUAA3 - 2766 - 279
23LEULEULEULEUDD3 - 2766 - 279
14LEULEUHISHISAA3 - 2756 - 278
24LEULEUHISHISEE3 - 2756 - 278
15LEULEULEULEUAA3 - 2766 - 279
25LEULEULEULEUFF3 - 2766 - 279
16ALAALALEULEUBB2 - 2765 - 279
26ALAALALEULEUCC2 - 2765 - 279
17ALAALALEULEUBB2 - 2765 - 279
27ALAALALEULEUDD2 - 2765 - 279
18LEULEUHISHISBB3 - 2756 - 278
28LEULEUHISHISEE3 - 2756 - 278
19ALAALAPHEPHEBB2 - 2825 - 285
29ALAALAPHEPHEFF2 - 2825 - 285
110METMETLEULEUCC1 - 2764 - 279
210METMETLEULEUDD1 - 2764 - 279
111LEULEUHISHISCC3 - 2756 - 278
211LEULEUHISHISEE3 - 2756 - 278
112METMETLEULEUCC1 - 2764 - 279
212METMETLEULEUFF1 - 2764 - 279
113LEULEUHISHISDD3 - 2756 - 278
213LEULEUHISHISEE3 - 2756 - 278
114METMETLEULEUDD1 - 2764 - 279
214METMETLEULEUFF1 - 2764 - 279
115LEULEUHISHISEE3 - 2756 - 278
215LEULEUHISHISFF3 - 2756 - 278

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

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Kanamycin B dioxygenase / Kanamycin biosynthesis protein J


Mass: 31841.100 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kanamyceticus (bacteria) / Gene: kanJ, kacB / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): MAGIC / References: UniProt: Q6L732, kanamycin B dioxygenase

-
Non-polymers , 5 types, 1039 molecules

#2: 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
#3: 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1007 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.3 Å3/Da / Density % sol: 77.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1:1 of 28% PEG4000 (w/v), 0.5 M lithium sulfate, 0.1 M HEPES, 0.1 M sodium acetate and 15mg/ml protein in 0.05 M bis-tris methane, 0.15 M NaCl; soaked with 0.05 M kanamycin B

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 17, 2017 / Details: Rosenbaum-Rock vertical focusing mirro
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.35→44.22 Å / Num. obs: 75259 / % possible obs: 95.11 % / Redundancy: 6.5 % / CC1/2: 0.734 / Rmerge(I) obs: 0.078 / Χ2: 1.21 / Net I/σ(I): 11.3
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.821 / Num. unique obs: 3923 / Χ2: 0.727

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6S0T

6s0t


Resolution: 2.36→44.22 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.081 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.239 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22465 3946 5 %RANDOM
Rwork0.18538 ---
obs0.18735 75259 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.172 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20.01 Å2
2--0.04 Å2-0 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 2.36→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13019 0 306 1007 14332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01313775
X-RAY DIFFRACTIONr_bond_other_d0.0050.01712482
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.64918939
X-RAY DIFFRACTIONr_angle_other_deg1.4211.57129015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42551669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67921.589711
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.012151956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.66815102
X-RAY DIFFRACTIONr_chiral_restr0.0670.21809
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215121
X-RAY DIFFRACTIONr_gen_planes_other0.0180.022689
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4733.766688
X-RAY DIFFRACTIONr_mcbond_other1.4733.7596687
X-RAY DIFFRACTIONr_mcangle_it2.555.6278353
X-RAY DIFFRACTIONr_mcangle_other2.555.6288354
X-RAY DIFFRACTIONr_scbond_it1.5224.0417087
X-RAY DIFFRACTIONr_scbond_other1.5224.0417088
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4555.99810587
X-RAY DIFFRACTIONr_long_range_B_refined6.65171.94156863
X-RAY DIFFRACTIONr_long_range_B_other6.58771.62156216
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87330.09
12B87330.09
21A87590.09
22C87590.09
31A88670.08
32D88670.08
41A87680.07
42E87680.07
51A88260.07
52F88260.07
61B87070.08
62C87070.08
71B87250.09
72D87250.09
81B86620.08
82E86620.08
91B87870.09
92F87870.09
101C87630.08
102D87630.08
111C87320.08
112E87320.08
121C88100.08
122F88100.08
131D87280.08
132E87280.08
141D88330.07
142F88330.07
151E87700.06
152F87700.06
LS refinement shellResolution: 2.36→2.417 Å
RfactorNum. reflection% reflection
Rfree0.336 180 -
Rwork0.269 3752 -
obs--63.77 %
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)
11.81870.6638-0.18993.30290.45252.70220.08-0.15520.2718-0.5156-0.29450.2903-0.3093-0.36810.21450.16440.1316-0.03050.2574-0.07130.074939.85245.33468.237
21.16990.24490.09892.0048-0.2411.11980.0789-0.0255-0.0510.27250.03820.0876-0.2021-0.059-0.11710.146-0.0150.08580.12720.00360.075834.55523.504140.786
31.12040.1999-0.08143.14910.01753.74270.0286-0.01580.03890.8821-0.1569-0.24920.16360.22530.12830.44130.0107-0.08530.08110.00240.032824.66966.835131.234
41.5245-0.08420.30351.1709-0.36593.1994-0.01720.2176-0.10320.1622-0.0462-0.08110.0102-0.02230.06340.1465-0.02570.07990.1671-0.03560.08062.0540.681105.123
51.1943-0.0811-0.97631.9084-0.14364.46770.031-0.14880.00990.53460.0593-0.2464-0.53110.3963-0.09040.4834-0.1124-0.18350.06940.02470.094214.7756.31366.819
62.7781-1.32481.4283.3539-2.02193.89510.48320.1919-0.491-0.4623-0.00420.4580.71790.0983-0.4790.18190.0244-0.08240.0225-0.05280.215310.37982.75793.131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 277
2X-RAY DIFFRACTION2B2 - 283
3X-RAY DIFFRACTION3C1 - 277
4X-RAY DIFFRACTION4D-1 - 277
5X-RAY DIFFRACTION5E3 - 276
6X-RAY DIFFRACTION6F1 - 285

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more