[English] 日本語
Yorodumi
- PDB-8hon: Crystal structure of the P450 BM3 heme domain mutant F87A in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hon
TitleCrystal structure of the P450 BM3 heme domain mutant F87A in complex with Im-C6-Tyr-Tyr
Components
  • Bifunctional cytochrome P450/NADPH--P450 reductase
  • Im-C6-Tyr-Tyr
KeywordsOXIDOREDUCTASE / Dual-functional small molecule / P450 heme domain / Complex
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / aromatase activity / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / cytosol
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsJiang, Y. / Dong, S. / Feng, Y. / Cong, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22207112 China
National Natural Science Foundation of China (NSFC)21977104 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Anchoring a Structurally Editable Proximal Cofactor-like Module to Construct an Artificial Dual-center Peroxygenase.
Authors: Qin, X. / Jiang, Y. / Yao, F. / Chen, J. / Kong, F. / Zhao, P. / Jin, L. / Cong, Z.
History
DepositionDec 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
C: Im-C6-Tyr-Tyr
D: Im-C6-Tyr-Tyr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9566
Polymers107,7234
Non-polymers1,2332
Water13,079726
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.673, 148.281, 64.703
Angle α, β, γ (deg.)90.00, 99.90, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Bifunctional cytochrome P450/NADPH--P450 reductase


Mass: 53352.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: BTA37_15100 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1Q8UP87, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Protein/peptide Im-C6-Tyr-Tyr


Mass: 508.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.38M MgCl2, 0.1M Tris 8.5, 12-18% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.01→74.14 Å / Num. obs: 66199 / % possible obs: 91.6 % / Redundancy: 2.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.048 / Rrim(I) all: 0.08 / Χ2: 0.41 / Net I/σ(I): 7.6 / Num. measured all: 166536
Reflection shellResolution: 2.01→2.12 Å / % possible obs: 94.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.369 / Num. measured all: 25375 / Num. unique obs: 9974 / CC1/2: 0.727 / Rpim(I) all: 0.282 / Rrim(I) all: 0.467 / Χ2: 0.35 / Net I/σ(I) obs: 2.5

-
Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimlessdata scaling
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→39.71 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2055 4965 7.54 %
Rwork0.1792 --
obs0.1812 65817 90.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 86 726 7980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087448
X-RAY DIFFRACTIONf_angle_d0.97810113
X-RAY DIFFRACTIONf_dihedral_angle_d19.0432743
X-RAY DIFFRACTIONf_chiral_restr0.2151085
X-RAY DIFFRACTIONf_plane_restr0.0061311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.24411680.23542087X-RAY DIFFRACTION92
2.03-2.050.27281590.23362018X-RAY DIFFRACTION92
2.05-2.080.29981650.22022055X-RAY DIFFRACTION92
2.08-2.110.27141680.2242058X-RAY DIFFRACTION92
2.11-2.130.24411670.22012040X-RAY DIFFRACTION93
2.13-2.160.27891740.21412107X-RAY DIFFRACTION93
2.16-2.190.2831710.21712079X-RAY DIFFRACTION94
2.19-2.230.25491680.22062062X-RAY DIFFRACTION93
2.23-2.260.27571720.22892099X-RAY DIFFRACTION94
2.26-2.30.29221700.21572088X-RAY DIFFRACTION94
2.3-2.340.24021720.19892106X-RAY DIFFRACTION94
2.34-2.380.19031700.19162071X-RAY DIFFRACTION93
2.38-2.430.25241690.18552076X-RAY DIFFRACTION93
2.43-2.480.24321700.19392064X-RAY DIFFRACTION93
2.48-2.530.23261670.22049X-RAY DIFFRACTION93
2.53-2.590.23951680.18462049X-RAY DIFFRACTION91
2.59-2.650.19951700.18782078X-RAY DIFFRACTION93
2.65-2.720.22471630.18571997X-RAY DIFFRACTION91
2.72-2.80.20221690.17682064X-RAY DIFFRACTION91
2.8-2.90.22311650.18052022X-RAY DIFFRACTION91
2.9-30.20311630.18282000X-RAY DIFFRACTION90
3-3.120.22431680.18682037X-RAY DIFFRACTION90
3.12-3.260.20431630.17742005X-RAY DIFFRACTION89
3.26-3.430.19561610.171967X-RAY DIFFRACTION88
3.43-3.650.20431600.16881954X-RAY DIFFRACTION88
3.65-3.930.18931580.1561942X-RAY DIFFRACTION87
3.93-4.320.14731560.14581900X-RAY DIFFRACTION85
4.32-4.950.13971590.14461954X-RAY DIFFRACTION86
4.95-6.230.20711560.17471921X-RAY DIFFRACTION86
6.23-39.710.15221560.16791903X-RAY DIFFRACTION83

+
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