[English] 日本語
Yorodumi
- PDB-9y35: Cytochrome P450 158A2 (CYP158A2) variant P354L bound to substrate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9y35
TitleCytochrome P450 158A2 (CYP158A2) variant P354L bound to substrate flaviolin
ComponentsBiflaviolin synthase CYP158A2
KeywordsOXIDOREDUCTASE / cytochrome P450 / flaviolin
Function / homology
Function and homology information


biflaviolin synthase / pigment metabolic process / 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
FLAVIOLIN / PROTOPORPHYRIN IX CONTAINING FE / Biflaviolin synthase CYP158A2
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGable, J.A. / Follmer, A.H. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57353 United States
CitationJournal: To Be Published
Title: Proximal Push in Cytochromes P450
Authors: Gable, J.A. / Follmer, A.H. / Poulos, T.L.
History
DepositionSep 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Biflaviolin synthase CYP158A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4534
Polymers44,4251
Non-polymers1,0293
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.300, 70.349, 101.352
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Biflaviolin synthase CYP158A2 / Cytochrome P450 158A2 / CYP158A2


Mass: 44424.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: cyp158a2, SCO1207 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FCA6, biflaviolin synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FLV / FLAVIOLIN / 2,5,7-TRIHYDROXYNAPHTHOQUINONE


Mass: 206.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: The protein sample had a concentration of 20 mg/mL in 20 mM Tris pH 7.4 and 2 mM flaviolin. The well solution was 0.1 M Bis-Tris pH 7.0 and 25% PEG 3350. Crystallization occurred by vapor ...Details: The protein sample had a concentration of 20 mg/mL in 20 mM Tris pH 7.4 and 2 mM flaviolin. The well solution was 0.1 M Bis-Tris pH 7.0 and 25% PEG 3350. Crystallization occurred by vapor diffusion in a hanging drop of 1:1, protein:well

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→28.97 Å / Num. obs: 246162 / % possible obs: 99.98 % / Redundancy: 11.7 % / Biso Wilson estimate: 16.19 Å2 / CC1/2: 0.998 / Net I/σ(I): 21.34
Reflection shellResolution: 2.2→2.32 Å / Mean I/σ(I) obs: 8.81 / Num. unique obs: 35190 / CC1/2: 0.96

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.97 Å / SU ML: 0.2827 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.5705
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2482 1040 4.94 %
Rwork0.1996 19997 -
obs0.202 21037 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 73 264 3393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01033208
X-RAY DIFFRACTIONf_angle_d1.29514389
X-RAY DIFFRACTIONf_chiral_restr0.0608478
X-RAY DIFFRACTIONf_plane_restr0.0363577
X-RAY DIFFRACTIONf_dihedral_angle_d14.81161183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.27411580.20992769X-RAY DIFFRACTION99.86
2.32-2.460.27981390.22822824X-RAY DIFFRACTION100
2.46-2.650.25811430.21152823X-RAY DIFFRACTION100
2.65-2.920.28761560.2142814X-RAY DIFFRACTION100
2.92-3.340.24841580.21662857X-RAY DIFFRACTION100
3.34-4.20.24781400.18832876X-RAY DIFFRACTION100
4.2-28.970.19521460.1693034X-RAY DIFFRACTION100

+
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