[English] 日本語
Yorodumi
- PDB-8w1j: Crystal Structure of a fatty acid decarboxylase from Corynebacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8w1j
TitleCrystal Structure of a fatty acid decarboxylase from Corynebacterium lipophiloflavum in complex with palmitic acid
ComponentsFatty acid decarboxylase
KeywordsOXIDOREDUCTASE / P450
Function / homology
Function and homology information


sterol 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 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PALMITIC ACID / Unspecific monooxygenase
Similarity search - Component
Biological speciesCorynebacterium lipophiloflavum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGeneroso, W.C. / Miyamoto, R.Y. / Murakami, M.T. / Zanphorlin, L.M.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2018/02865-2 Brazil
Sao Paulo Research Foundation (FAPESP)2019/08855-1 Brazil
Sao Paulo Research Foundation (FAPESP)2021/14410-2 Brazil
CitationJournal: Nat Commun / Year: 2025
Title: Coordinated conformational changes in P450 decarboxylases enable hydrocarbons production from renewable feedstocks.
Authors: Generoso, W.C. / Alvarenga, A.H.S. / Simoes, I.T. / Miyamoto, R.Y. / Melo, R.R. / Guilherme, E.P.X. / Mandelli, F. / Santos, C.A. / Prata, R. / Santos, C.R.D. / Colombari, F.M. / Morais, M.A. ...Authors: Generoso, W.C. / Alvarenga, A.H.S. / Simoes, I.T. / Miyamoto, R.Y. / Melo, R.R. / Guilherme, E.P.X. / Mandelli, F. / Santos, C.A. / Prata, R. / Santos, C.R.D. / Colombari, F.M. / Morais, M.A.B. / Pimentel Fernandes, R. / Persinoti, G.F. / Murakami, M.T. / Zanphorlin, L.M.
History
DepositionFeb 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid decarboxylase
B: Fatty acid decarboxylase
C: Fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,65718
Polymers148,1803
Non-polymers3,47715
Water18,6641036
1
A: Fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6507
Polymers49,3931
Non-polymers1,2576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4505
Polymers49,3931
Non-polymers1,0574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5576
Polymers49,3931
Non-polymers1,1635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.926, 171.018, 122.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Fatty acid decarboxylase


Mass: 49393.383 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium lipophiloflavum (bacteria)
Gene: HMPREF0298_0515
Details (production host): pGTF2 which encodes GroEL, GroES and Tig chaperones
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0XPZ5

-
Non-polymers , 7 types, 1051 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1036 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30 % (w/v) PEG4000, 0.2 M MgCl2, 0.1 M HEPES pH 7.5. The proteins were concentrated in GF buffer with 5 % glycerol and 1 mM palmitic acid.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.8→49.74 Å / Num. obs: 152317 / % possible obs: 100 % / Redundancy: 13.53 % / CC1/2: 0.99 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.16 / Net I/σ(I): 4.94
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.910.845185980.4031.0891
1.91-2.040.54167960.6430.6921
2.04-2.20.349148270.8270.4441
2.2-2.410.24144680.9130.3031
2.41-2.70.172132150.9490.2171
2.7-3.110.119113790.9750.151
3.11-3.810.06891150.9890.0861
3.81-5.370.04866920.9940.061
5.37-49.740.04938380.9950.0611

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.74 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 7611 5 %
Rwork0.1758 --
obs0.1776 152212 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9705 0 238 1036 10979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110214
X-RAY DIFFRACTIONf_angle_d1.01113885
X-RAY DIFFRACTIONf_dihedral_angle_d14.4363758
X-RAY DIFFRACTIONf_chiral_restr0.0581492
X-RAY DIFFRACTIONf_plane_restr0.0111845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.45532500.44334746X-RAY DIFFRACTION100
1.82-1.840.42452530.38194811X-RAY DIFFRACTION100
1.84-1.860.35822490.32544731X-RAY DIFFRACTION100
1.86-1.890.31472520.29554790X-RAY DIFFRACTION100
1.89-1.910.3032520.27554788X-RAY DIFFRACTION100
1.91-1.940.29032550.26264833X-RAY DIFFRACTION100
1.94-1.970.29922500.26694746X-RAY DIFFRACTION100
1.97-20.32232510.27334770X-RAY DIFFRACTION100
2-2.030.28842510.27444768X-RAY DIFFRACTION100
2.03-2.060.30722530.24034818X-RAY DIFFRACTION100
2.06-2.10.25222510.22284761X-RAY DIFFRACTION100
2.1-2.130.24832540.20194825X-RAY DIFFRACTION100
2.13-2.180.2292520.19824783X-RAY DIFFRACTION100
2.18-2.220.23972530.18694822X-RAY DIFFRACTION100
2.22-2.270.21212520.17484789X-RAY DIFFRACTION100
2.27-2.320.23022530.16744796X-RAY DIFFRACTION100
2.32-2.380.20692540.17124832X-RAY DIFFRACTION100
2.38-2.440.22292520.16684807X-RAY DIFFRACTION100
2.44-2.520.22222520.16914791X-RAY DIFFRACTION100
2.52-2.60.23492560.17344849X-RAY DIFFRACTION100
2.6-2.690.21682520.17284789X-RAY DIFFRACTION100
2.69-2.80.21952530.1754812X-RAY DIFFRACTION100
2.8-2.920.22542540.17344826X-RAY DIFFRACTION100
2.92-3.080.20672550.16544853X-RAY DIFFRACTION100
3.08-3.270.19912550.16644838X-RAY DIFFRACTION100
3.27-3.520.1922560.16364865X-RAY DIFFRACTION100
3.52-3.880.18512560.14824866X-RAY DIFFRACTION100
3.88-4.440.1442580.12734892X-RAY DIFFRACTION100
4.44-5.590.16392590.13444928X-RAY DIFFRACTION100
5.59-49.740.18092680.15275076X-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