[English] 日本語
Yorodumi
- PDB-9duj: Crystal structure of RufO in complex with (Nle)RYLH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9duj
TitleCrystal structure of RufO in complex with (Nle)RYLH
Components
  • Cytochrome P450
  • NLE-ARG-TYR-LEU-HIS
KeywordsOXIDOREDUCTASE / Rufomycin biosynthesis / cytochrome P450 enzyme / RiPP-producing enzyme / nitrating heme enzyme / peptide bound
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces atratus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsNolan, K. / Wang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM147510 United States
CitationJournal: Acs Catalysis / Year: 2025
Title: Molecular Basis for Peptide Nitration by a Novel Cytochrome P450 Enzyme in RiPP Biosynthesis
Authors: Nolan, K. / Usai, R. / Li, B. / Jordan, S. / Wang, Y.
History
DepositionOct 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450
B: NLE-ARG-TYR-LEU-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,21810
Polymers44,1462
Non-polymers1,0728
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-43 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.258, 77.833, 89.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Cytochrome P450


Mass: 43442.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces atratus (bacteria) / Gene: rufO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A224AU14
#2: Protein/peptide NLE-ARG-TYR-LEU-HIS


Mass: 702.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces atratus (bacteria)

-
Non-polymers , 5 types, 524 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3000, 100 mM Tris base/HCl pH 7.0, 200 mM Calcium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 62065 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.035 / Rrim(I) all: 0.124 / Χ2: 2.312 / Net I/σ(I): 9.5 / Num. measured all: 760297
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.51-1.5410.50.63130510.9250.980.1990.6620.859100
1.54-1.56120.60930480.9440.9850.1770.6350.899100
1.56-1.5913.20.55730940.9640.9910.1560.5790.989100
1.59-1.6313.30.50530520.9680.9920.1410.5251.104100
1.63-1.6613.40.46230640.9720.9930.1290.481.161100
1.66-1.713.30.41430840.9730.9930.1160.431.313100
1.7-1.7413.30.36130540.9790.9950.1020.3761.49100
1.74-1.7913.10.31430670.9820.9950.090.3271.695100
1.79-1.8412.80.27430780.9850.9960.0790.2861.804100
1.84-1.912.70.24330690.9870.9970.0710.2532.034100
1.9-1.97120.20830650.9910.9980.0630.2172.265100
1.97-2.0510.80.1831130.9910.9980.0580.1892.593100
2.05-2.1411.20.14830870.9930.9980.0470.1552.872100
2.14-2.2612.60.13130850.9950.9990.0380.1373.087100
2.26-2.412.80.11331240.9960.9990.0330.1183.296100
2.4-2.5812.50.10131180.9970.9990.030.1053.48100
2.58-2.8412.30.09131250.9970.9990.0270.0953.752100
2.84-3.2511.60.07931520.9970.9990.0240.0834.066100
3.25-4.19.60.06731950.9980.9990.0220.0714.29799.9
4.1-5012.10.05933400.99810.0170.0623.77299.8

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→47.58 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 1999 3.23 %
Rwork0.1638 --
obs0.1646 61898 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 29 516 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053266
X-RAY DIFFRACTIONf_angle_d0.874482
X-RAY DIFFRACTIONf_dihedral_angle_d13.2471208
X-RAY DIFFRACTIONf_chiral_restr0.05491
X-RAY DIFFRACTIONf_plane_restr0.009601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.20691330.18973999X-RAY DIFFRACTION94
1.55-1.590.22211430.17444243X-RAY DIFFRACTION100
1.59-1.640.2141410.16974241X-RAY DIFFRACTION100
1.64-1.690.19351420.16434275X-RAY DIFFRACTION100
1.69-1.750.19021420.16494246X-RAY DIFFRACTION100
1.75-1.820.19651440.16554291X-RAY DIFFRACTION100
1.82-1.90.20971400.17334227X-RAY DIFFRACTION100
1.9-20.23381430.16574293X-RAY DIFFRACTION100
2-2.130.19861430.15934253X-RAY DIFFRACTION100
2.13-2.290.18151440.15684327X-RAY DIFFRACTION100
2.29-2.520.20271440.16434306X-RAY DIFFRACTION100
2.52-2.890.18741440.16624337X-RAY DIFFRACTION100
2.89-3.640.17381460.16164335X-RAY DIFFRACTION99
3.64-47.580.17321500.15954526X-RAY DIFFRACTION99

+
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