[English] 日本語
Yorodumi
- PDB-9nns: Flavin-dependent N5-ornithine monooxygenase EtcB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nns
TitleFlavin-dependent N5-ornithine monooxygenase EtcB
ComponentsL-lysine N6-monooxygenase MbtG
KeywordsFLAVOPROTEIN / FAD-dependent / erythrochelin / monooxygenase
Function / homologyL-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / biosynthetic process / FAD/NAD(P)-binding domain superfamily / ADENOSINE-5'-DIPHOSPHATE / L-lysine N6-monooxygenase MbtG
Function and homology information
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLi, Y. / Liu, X. / Smith, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM138396 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)DK042303 United States
CitationJournal: Structure / Year: 2025
Title: Redefining the role of the EryM acetyltransferase in natural product biosynthetic pathways.
Authors: Li, Y. / Liu, X. / Harris, N.R. / Roberts, J.R. / Valdivia, E.M. / Ji, X. / Smith, J.L.
History
DepositionMar 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-lysine N6-monooxygenase MbtG
B: L-lysine N6-monooxygenase MbtG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7884
Polymers101,9332
Non-polymers8542
Water19811
1
A: L-lysine N6-monooxygenase MbtG
B: L-lysine N6-monooxygenase MbtG
hetero molecules

A: L-lysine N6-monooxygenase MbtG
B: L-lysine N6-monooxygenase MbtG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,5758
Polymers203,8664
Non-polymers1,7094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12890 Å2
ΔGint-85 kcal/mol
Surface area74110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.725, 83.306, 150.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 7 through 60 or (resid 61...
d_2ens_1(chain "B" and (resid 7 through 176 or resid 178...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERGLYGLYAA7 - 18426 - 203
d_12HISHISLEULEUAA189 - 193208 - 212
d_13ARGARGGLYGLYAA207 - 226226 - 245
d_14ALAALAALAALAAA231250
d_15SERSERSERSERAA234253
d_16ASPASPILEILEAA247 - 254266 - 273
d_17VALVALASNASNAA286 - 313305 - 332
d_18LEULEUGLUGLUAA318 - 319337 - 338
d_19ARGARGGLUGLUAA328 - 332347 - 351
d_110LEULEULEULEUAA342361
d_111VALVALTHRTHRAA347 - 432366 - 451
d_112ADPADPADPADPAC501
d_21SERSERASNASNBB7 - 17626 - 195
d_22PROPROGLYGLYBB178 - 226197 - 245
d_23ALAALAALAALABB235254
d_24SERSERSERSERBB238257
d_25ASPASPASNASNBB247 - 313266 - 332
d_26LEULEUGLUGLUBB318 - 332337 - 351
d_27LEULEULEULEUBB334353
d_28VALVALILEILEBB347 - 407366 - 426
d_29LEULEUTHRTHRBB411 - 432430 - 451
d_210ADPADPADPADPBD501

NCS oper: (Code: givenMatrix: (-0.82914827377, -0.0380377190609, 0.557733154862), (0.0353783005046, -0.999252932473, -0.0155548319985), (0.557908160863, 0.0068343890538, 0.829874553875)Vector: 27. ...NCS oper: (Code: given
Matrix: (-0.82914827377, -0.0380377190609, 0.557733154862), (0.0353783005046, -0.999252932473, -0.0155548319985), (0.557908160863, 0.0068343890538, 0.829874553875)
Vector: 27.5403595165, 46.2354554381, -8.4274373526)

-
Components

#1: Protein L-lysine N6-monooxygenase MbtG / Lysine 6-N-hydroxylase / Lysine N6-hydroxylase / Lysine-N-oxygenase / Mycobactin synthase protein G


Mass: 50966.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: SACE_3033 / Production host: Escherichia coli (E. coli)
References: UniProt: A4FE36, L-lysine N6-monooxygenase (NADPH)
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Tris, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→41.65 Å / Num. obs: 27141 / % possible obs: 99.86 % / Redundancy: 15.4 % / Biso Wilson estimate: 86.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.6
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.982 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2640 / CC1/2: 0.736

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→41.65 Å / SU ML: 0.4969 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.6804
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.35 808 4.07 %
Rwork0.2531 19057 -
obs0.2571 19865 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.74 Å2
Refinement stepCycle: LAST / Resolution: 3→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 54 11 5591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00865678
X-RAY DIFFRACTIONf_angle_d1.28717714
X-RAY DIFFRACTIONf_chiral_restr0.0616874
X-RAY DIFFRACTIONf_plane_restr0.0091014
X-RAY DIFFRACTIONf_dihedral_angle_d16.40031997
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.67126617402 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.40451300.29483120X-RAY DIFFRACTION99.88
3.19-3.430.34391370.27113129X-RAY DIFFRACTION100
3.43-3.780.35391280.27593149X-RAY DIFFRACTION99.76
3.78-4.330.3751340.23973132X-RAY DIFFRACTION99.57
4.33-5.450.34161380.24553201X-RAY DIFFRACTION99.94
5.45-41.650.33811410.24783326X-RAY DIFFRACTION99.28

+
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