[English] 日本語
Yorodumi
- PDB-8euk: cytochrome P450terp (cyp108A1) bound to ethylene glycol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8euk
Titlecytochrome P450terp (cyp108A1) bound to ethylene glycol
ComponentsCytochrome P450-terp
KeywordsOXIDOREDUCTASE / monooxygenase / complex / substrate / heme
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm
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 / Cytochrome P450-terp
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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)GM131920 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Cooperative Substrate Binding Controls Catalysis in Bacterial Cytochrome P450terp (CYP108A1).
Authors: Gable, J.A. / Poulos, T.L. / Follmer, A.H.
History
DepositionOct 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 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-terp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,51014
Polymers50,1491
Non-polymers1,36113
Water5,062281
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)68.730, 68.730, 457.039
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein Cytochrome P450-terp / Cytochrome P450terp / Cytochrome P450 108


Mass: 50148.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Gene: cyp108, terPC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P33006, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.06 M magnesium chloride hexahyrate, 0.06 M calcium chloride dihydrate, 0.1 M sodium HEPES and MOPS (acid) pH 7.5, 20% v/v ethylene glycol, 10% v/v PEG 8000

-
Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→59.52 Å / Num. obs: 46098 / % possible obs: 99.92 % / Redundancy: 20.1 % / Biso Wilson estimate: 27.62 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.01765 / Net I/σ(I): 27.93
Reflection shellResolution: 1.984→2.055 Å / Mean I/σ(I) obs: 11.55 / Num. unique obs: 4465 / CC1/2: 0.995 / Rpim(I) all: 0.04957 / % possible all: 99.98

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CPT

1cpt


Resolution: 1.98→59.52 Å / SU ML: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2064 2383 5.17 %
Rwork0.18 43697 -
obs0.1814 46080 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.07 Å2
Refinement stepCycle: LAST / Resolution: 1.98→59.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 91 281 3672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01123476
X-RAY DIFFRACTIONf_angle_d1.35024707
X-RAY DIFFRACTIONf_chiral_restr0.0812497
X-RAY DIFFRACTIONf_plane_restr0.0053614
X-RAY DIFFRACTIONf_dihedral_angle_d14.36591279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.020.2181230.19352535X-RAY DIFFRACTION99.96
2.02-2.070.211190.19112487X-RAY DIFFRACTION100
2.07-2.120.21951450.18882477X-RAY DIFFRACTION100
2.12-2.170.20611530.18382505X-RAY DIFFRACTION99.96
2.17-2.230.23131530.17692485X-RAY DIFFRACTION99.92
2.23-2.290.2141570.19052531X-RAY DIFFRACTION99.96
2.29-2.370.20791310.17492508X-RAY DIFFRACTION99.96
2.37-2.450.26351390.18852540X-RAY DIFFRACTION100
2.45-2.550.20541280.17542522X-RAY DIFFRACTION99.96
2.55-2.670.20081390.17752550X-RAY DIFFRACTION99.96
2.67-2.810.22721340.18592532X-RAY DIFFRACTION100
2.81-2.980.20631600.17732593X-RAY DIFFRACTION99.96
2.98-3.210.22661480.18632547X-RAY DIFFRACTION99.96
3.21-3.540.20371330.18392613X-RAY DIFFRACTION100
3.54-4.050.20021520.17132644X-RAY DIFFRACTION99.93
4.05-5.10.1821310.16422687X-RAY DIFFRACTION99.96
5.1-59.520.18771380.19082941X-RAY DIFFRACTION99.26

+
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