[English] 日本語
Yorodumi
- PDB-3el3: Distinct Monooxygenase and Farnesene Synthase Active Sites in Cyt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3el3
TitleDistinct Monooxygenase and Farnesene Synthase Active Sites in Cytochrome P450 170A1
ComponentsPutative cytochrome P450
KeywordsOXIDOREDUCTASE / streptomyces / Cytochrome P450 oxidoreductase / CYP170A1 / antibiotic biosynthesis / farnesene synthase / Heme / Iron / Metal-binding / Monooxygenase
Function / homology
Function and homology information


epi-isozizaene 5-monooxygenase / beta-farnesene synthase / sesquiterpene synthase activity / sesquiterpene biosynthetic process / ketone biosynthetic process / terpene synthase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic process / monooxygenase activity / iron ion binding ...epi-isozizaene 5-monooxygenase / beta-farnesene synthase / sesquiterpene synthase activity / sesquiterpene biosynthetic process / ketone biosynthetic process / terpene synthase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic process / monooxygenase activity / iron ion binding / heme binding / cytosol
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EL3 / PROTOPORPHYRIN IX CONTAINING FE / Bifunctional albaflavenone monooxygenase/terpene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZhao, B. / Waterman, M.R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of albaflavenone monooxygenase containing a moonlighting terpene synthase active site
Authors: Zhao, B. / Lei, L. / Vassylyev, D.G. / Lin, X. / Cane, D.E. / Kelly, S.L. / Yuan, H. / Lamb, D.C. / Waterman, M.R.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative cytochrome P450
B: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7258
Polymers103,6742
Non-polymers2,0506
Water0
1
A: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8624
Polymers51,8371
Non-polymers1,0253
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8624
Polymers51,8371
Non-polymers1,0253
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.548, 107.548, 141.648
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Putative cytochrome P450 /


Mass: 51837.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K498
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-EL3 / (3S,3aR,6S)-3,7,7,8-tetramethyl-2,3,4,5,6,7-hexahydro-1H-3a,6-methanoazulene / 2,2,3,7R-tetramethyl-1R,8S-tricyclo-[6.2.1.0(4,8)]undec-3-en


Mass: 204.351 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M ammonium sulphate, 0.1M Tris-HCl pH7.0, 1mM epi-isozizaene, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2008
RadiationMonochromator: Si 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 12957 / % possible obs: 80.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Rsym value: 0.039
Reflection shellResolution: 3.3→3.41 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.37 / Num. unique all: 1024 / Rsym value: 0.259 / % possible all: 64.3

-
Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DBG

3dbg


Resolution: 3.3→35.48 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.2 / σ(I): 0.2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 1009 -RANDOM
Rwork0.2279 ---
obs0.2279 11703 83.5 %-
all-14024 --
Displacement parametersBiso mean: 88.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å20 Å20 Å2
2--2.77 Å20 Å2
3----5.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.68 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å1.22 Å
Refinement stepCycle: LAST / Resolution: 3.3→35.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6406 0 146 0 6552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_dihedral_angle_d23
LS refinement shellResolution: 3.3→3.45 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.3919 58 -
Rwork0.4007 --
obs-622 69.3 %

+
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