[English] 日本語
Yorodumi
- PDB-8fid: Crystal Structure of Erwinia tracheiphila CYP114 in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fid
TitleCrystal Structure of Erwinia tracheiphila CYP114 in complex with ent-kaurenoic acid (Crystal Form 2)
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / gibberellin
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-NE4 / Cytochrome P450
Similarity search - Component
Biological speciesErwinia tracheiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsStewart Jr., C.E. / Nagel, R.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131885 United States
German Research Foundation (DFG)NA 1261/1-2 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Dual factors required for cytochrome-P450-mediated hydrocarbon ring contraction in bacterial gibberellin phytohormone biosynthesis.
Authors: Nagel, R. / Alexander, L.E. / Stewart Jr., C.E. / Peters, R.J.
History
DepositionDec 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8003
Polymers48,8811
Non-polymers9192
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.460, 70.030, 59.280
Angle α, β, γ (deg.)90.000, 95.250, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Cytochrome P450


Mass: 48881.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia tracheiphila (bacteria) / Gene: SY86_19565 / Plasmid: pET101 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Star / References: UniProt: A0A0M2KDV0
#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-NE4 / (8alpha,9beta,10alpha,13alpha)-kaur-16-en-18-oic acid / ent-kaurenoic acid


Mass: 302.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.35 % / Mosaicity: 0.36 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: 25% PEG4000, 0.1M MES/Tris pH5.6, 0.15M Ammonium sulfate, 10mM Cadmium chloride hydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2018 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→59.031 Å / Num. obs: 47323 / % possible obs: 98.6 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.071 / Rrim(I) all: 0.148 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.7341.1221015925260.1060.6141.2851.398.9
8.98-59.034.40.05815093440.9940.030.06520.199.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.7 Å59.03 Å
Translation1.7 Å59.03 Å

-
Processing

Software
NameVersionClassification
MOSFLM7.2data reduction
Aimless0.6.2data scaling
PHASER2.8.0phasing
PHENIX1.14refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RLP

7rlp
PDB Unreleased entry


Resolution: 1.83→59.031 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 1593 4.22 %
Rwork0.1876 36123 -
obs0.1892 37716 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.62 Å2 / Biso mean: 40.8251 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 1.83→59.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 124 255 3607
Biso mean--25.01 42.89 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.83-1.88910.40041410.3513323898
1.8891-1.95660.3041450.3018325698
1.9566-2.0350.31851450.2604330199
2.035-2.12760.311460.2246328298
2.1276-2.23980.22041410.1936323998
2.2398-2.38010.21341440.1787325798
2.3801-2.56390.22511460.1797330099
2.5639-2.82190.221450.1656329399
2.8219-3.23020.2241450.1774328398
3.2302-4.06960.21131460.1608330698
4.0696-59.0310.19311490.175336898

+
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://pdbjlvh1.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