[English] 日本語
Yorodumi
- PDB-6s0v: The crystal structure of kanamycin B dioxygenase (KanJ) from Stre... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s0v
TitleThe crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, neamine and sulfate
ComponentsKanamycin B dioxygenase
KeywordsMETAL BINDING PROTEIN / non-heme iron dioxygenase / alpha-ketoglutarate dioxygenase / Kanamycin biosynthesis / KanJ / OXIDOREDUCTASE
Function / homologykanamycin B dioxygenase / : / kanamycin biosynthetic process / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / 2-oxoglutarate-dependent dioxygenase activity / NICKEL (II) ION / Chem-XXX / Kanamycin B dioxygenase
Function and homology information
Biological speciesStreptomyces kanamyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 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) 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 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 25, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.title / _citation_author.identifier_ORCID
Revision 2.2Feb 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 2.3Mar 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 2.4Jan 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)195,06236
Polymers191,0476
Non-polymers4,01530
Water2,612145
1
A: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5106
Polymers31,8411
Non-polymers6695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4145
Polymers31,8411
Non-polymers5734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4145
Polymers31,8411
Non-polymers5734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6067
Polymers31,8411
Non-polymers7656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5106
Polymers31,8411
Non-polymers6695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kanamycin B dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6067
Polymers31,8411
Non-polymers7656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.467, 185.250, 110.460
Angle α, β, γ (deg.)90.00, 94.68, 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
11ALAALAPHEPHEAA2 - 2825 - 285
21ALAALAPHEPHEBB2 - 2825 - 285
12ALAALALEULEUAA2 - 2765 - 279
22ALAALALEULEUCC2 - 2765 - 279
13ALAALAPHEPHEAA2 - 2825 - 285
23ALAALAPHEPHEDD2 - 2825 - 285
14LEULEUASPASPAA3 - 2726 - 275
24LEULEUASPASPEE3 - 2726 - 275
15ALAALAPHEPHEAA2 - 2825 - 285
25ALAALAPHEPHEFF2 - 2825 - 285
16METMETLEULEUBB1 - 2764 - 279
26METMETLEULEUCC1 - 2764 - 279
17METMETVALVALBB1 - 2844 - 287
27METMETVALVALDD1 - 2844 - 287
18LEULEUASPASPBB3 - 2726 - 275
28LEULEUASPASPEE3 - 2726 - 275
19METMETVALVALBB1 - 2844 - 287
29METMETVALVALFF1 - 2844 - 287
110ALAALALEULEUCC0 - 2763 - 279
210ALAALALEULEUDD0 - 2763 - 279
111LEULEUASPASPCC3 - 2726 - 275
211LEULEUASPASPEE3 - 2726 - 275
112METMETLEULEUCC1 - 2764 - 279
212METMETLEULEUFF1 - 2764 - 279
113LEULEUASPASPDD3 - 2726 - 275
213LEULEUASPASPEE3 - 2726 - 275
114METMETVALVALDD1 - 2844 - 287
214METMETVALVALFF1 - 2844 - 287
115LEULEUASPASPEE3 - 2726 - 275
215LEULEUASPASPFF3 - 2726 - 275

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

-
Components

#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
#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.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Sugar
ChemComp-XXX / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside / (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA N-3,4-DIOL / NEOMYCIN A / NEAMINE / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-glucoside


Type: D-saccharide / Mass: 322.358 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26N4O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.36 Å3/Da / Density % sol: 77.06 %
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 0.02 M neamine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97938 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2018 / Details: Bimorph K-B pair
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 3→48.54 Å / Num. obs: 40424 / % possible obs: 90.74 % / Redundancy: 5.2 % / CC1/2: 0.982 / Rmerge(I) obs: 0.126 / Net I/σ(I): 6.6
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.947 / Num. unique obs: 2006 / CC1/2: 0.661

-
Processing

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

6s0t


Resolution: 3→48.54 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.888 / SU B: 41.197 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.448 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22824 1793 4.9 %RANDOM
Rwork0.19973 ---
obs0.20112 34821 90.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.168 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å2-0 Å2-0.36 Å2
2--0.22 Å20 Å2
3----1.6 Å2
Refinement stepCycle: 1 / Resolution: 3→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13104 0 228 145 13477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01313751
X-RAY DIFFRACTIONr_bond_other_d0.0040.01712483
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.64718895
X-RAY DIFFRACTIONr_angle_other_deg1.3371.5728996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56851674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50121.547711
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.403151958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.41215102
X-RAY DIFFRACTIONr_chiral_restr0.0580.21786
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215166
X-RAY DIFFRACTIONr_gen_planes_other0.0170.022704
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_it1.5843.8976720
X-RAY DIFFRACTIONr_mcbond_other1.5843.8976719
X-RAY DIFFRACTIONr_mcangle_it2.7945.8378386
X-RAY DIFFRACTIONr_mcangle_other2.7945.8378387
X-RAY DIFFRACTIONr_scbond_it1.7344.1647031
X-RAY DIFFRACTIONr_scbond_other1.7344.1657032
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7526.18610510
X-RAY DIFFRACTIONr_long_range_B_refined9.52474.48755909
X-RAY DIFFRACTIONr_long_range_B_other9.52674.48855907
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)
11A87030.09
12B87030.09
21A85570.09
22C85570.09
31A86850.08
32D86850.08
41A84920.07
42E84920.07
51A86390.09
52F86390.09
61B85490.09
62C85490.09
71B86240.09
72D86240.09
81B84730.07
82E84730.07
91B87120.1
92F87120.1
101C86220.09
102D86220.09
111C85020.08
112E85020.08
121C85680.1
122F85680.1
131D85010.07
132E85010.07
141D87650.09
142F87650.09
151E85290.07
152F85290.07
LS refinement shellResolution: 3.002→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 71 -
Rwork0.292 1532 -
obs--54.38 %
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)
10.89730.4551-0.0672.2808-0.39812.06940.1474-0.0680.1834-0.2366-0.23690.1498-0.0144-0.04630.08950.08860.04590.06550.1561-0.0210.238640.19744.5968.486
20.5829-0.12820.06541.2482-0.3120.95140.1010.0534-0.09530.1858-0.0070.0848-0.067-0.0277-0.09410.1122-0.0150.09990.0955-0.00930.230435.67722.678141.224
30.41030.28670.26312.27190.26882.19510.03530.09130.06080.5568-0.0609-0.11580.30850.15540.02560.26260.0526-0.03990.0929-0.02560.166726.16765.97131.544
41.3634-0.04460.15251.32550.08611.7588-0.05550.1296-0.07560.1735-0.008-0.07420.0234-0.00650.06350.10310.00760.11190.07110.00260.19142.98939.764105.42
51.2171-0.0356-0.20260.5527-0.00482.97270.0091-0.0572-0.0990.10630.0774-0.041-0.29780.2604-0.08650.134-0.0599-0.03170.0650.02710.207115.1646.0567.158
61.3703-0.93460.67642.2519-1.81863.97290.3439-0.0067-0.1721-0.44080.02560.23410.58820.1485-0.36950.16880.0071-0.02980.0139-0.03080.241411.4681.65793.454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 283
2X-RAY DIFFRACTION2B1 - 284
3X-RAY DIFFRACTION3C0 - 277
4X-RAY DIFFRACTION4D-1 - 285
5X-RAY DIFFRACTION5E3 - 273
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