[English] 日本語
Yorodumi
- PDB-7xbo: Crystal Structure of 10-dml-bound cytochrome P450 PikC with the u... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xbo
TitleCrystal Structure of 10-dml-bound cytochrome P450 PikC with the unnatural amino acid p-Acetyl-L-Phenylalanine incorporated at position 238
ComponentsCytochrome P450 monooxygenase PikC
KeywordsOXIDOREDUCTASE / 10-dml-bound / PikC / unnatural amino acid
Function / homology
Function and homology information


pikromycin synthase / macrolide biosynthetic 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
Chem-E4H / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Cytochrome P450 monooxygenase PikC
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, G.B. / Pan, Y.J. / Li, S.Y. / Gao, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000039 China
National Natural Science Foundation of China (NSFC)32025001 China
National Natural Science Foundation of China (NSFC)31872729 China
CitationJournal: Nat Commun / Year: 2023
Title: New mechanistic insight of cytochrome P450 PikC gained from site-specific mutagenesis by non-coding amino acids
Authors: Pan, Y.J. / Li, G.B. / Gao, X. / Li, S.Y.
History
DepositionMar 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 monooxygenase PikC
B: Cytochrome P450 monooxygenase PikC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,55716
Polymers98,7822
Non-polymers2,77514
Water8,647480
1
A: Cytochrome P450 monooxygenase PikC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8709
Polymers49,3911
Non-polymers1,4798
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-21 kcal/mol
Surface area16500 Å2
MethodPISA
2
B: Cytochrome P450 monooxygenase PikC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6867
Polymers49,3911
Non-polymers1,2956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-21 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.119, 108.480, 153.147
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

-
Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450 monooxygenase PikC / Cytochrome P450 monooxygenase PicK / Narbomycin C-12 hydroxylase / Pikromycin synthase CYP107L1


Mass: 49390.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: pikC, picK / Production host: Escherichia coli (E. coli) / References: UniProt: O87605, pikromycin synthase

-
Non-polymers , 5 types, 494 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-E4H / (3R,4S,5S,7R,9E,11R,12R)-12-ETHYL-4-HYDROXY-3,5,7,11-TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE


Mass: 296.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H28O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.2M (NH4)2SO4, 0.1M Bis-TRIS, pH 5.8, 19% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 50823 / % possible obs: 98.9 % / Redundancy: 11.8 % / Biso Wilson estimate: 29.64 Å2 / CC1/2: 0.995 / Net I/σ(I): 14.5
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 4739 / CC1/2: 0.783

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVJ

2bvj


Resolution: 2.2→32.7 Å / SU ML: 0.204 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 1999 4.46 %
Rwork0.179 42809 -
obs0.1805 44808 86.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 0 190 480 6811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266477
X-RAY DIFFRACTIONf_angle_d0.60438841
X-RAY DIFFRACTIONf_chiral_restr0.0407975
X-RAY DIFFRACTIONf_plane_restr0.00491153
X-RAY DIFFRACTIONf_dihedral_angle_d16.13092407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.2565950.19252042X-RAY DIFFRACTION58.39
2.26-2.320.29111060.20042277X-RAY DIFFRACTION65.56
2.32-2.390.23681130.2042393X-RAY DIFFRACTION69.4
2.39-2.460.27331190.20942559X-RAY DIFFRACTION73.77
2.46-2.550.28291240.20742679X-RAY DIFFRACTION77.65
2.55-2.650.21521370.19632936X-RAY DIFFRACTION83.48
2.65-2.770.27551480.20953151X-RAY DIFFRACTION90.26
2.77-2.920.26141570.21083369X-RAY DIFFRACTION97.16
2.92-3.10.27061640.20173512X-RAY DIFFRACTION99.92
3.1-3.340.20681650.18313529X-RAY DIFFRACTION100
3.34-3.680.17691640.17073513X-RAY DIFFRACTION99.97
3.68-4.210.17841660.15063548X-RAY DIFFRACTION100
4.21-5.30.18591670.14763587X-RAY DIFFRACTION99.97
5.3-32.70.18221740.18023714X-RAY DIFFRACTION98.78

+
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