8JC3 | pdb_00008jc3

Crystal structure of the P450 BM3 heme domain mutant F87A-T268V in complex with Pyd-N-C4-Phe and hydroxylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted LXOClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

C(sp3)-H hydroxylation of Broad-Spectrum Alkanes Catalyzed by an Artificial P450 Peroxygenase Driven by omega-Pyridyl Fatty Acyl Amino Acids.

Qin, X.Jiang, Y.Chen, J.Yao, F.Jin, L.Cong, Z.

(2023) Mol Catal 550


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional cytochrome P450/NADPH--P450 reductaseA [auth B],
B [auth A]
465Priestia megaterium NBRC 15308 = ATCC 14581Mutation(s): 2 
Gene Names: cyp102A1cyp102BG04_163
EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19))
Explore P14779 
Go to UniProtKB:  P14779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14779
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth B],
I [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LXO (Subject of Investigation/LOI)
Query on LXO

Download Ideal Coordinates CCD File 
E [auth B],
G [auth B],
K [auth A],
M [auth A]
4-(pyridin-4-ylamino)butanoic acid
C9 H12 N2 O2
HPDCDJWQNLPXFS-UHFFFAOYSA-N
PHE
Query on PHE

Download Ideal Coordinates CCD File 
F [auth B],
H [auth B],
L [auth A],
N [auth A]
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
HOA (Subject of Investigation/LOI)
Query on HOA

Download Ideal Coordinates CCD File 
D [auth B],
J [auth A]
HYDROXYAMINE
H3 N O
AVXURJPOCDRRFD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.556α = 90
b = 147.58β = 100.21
c = 64.598γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted LXOClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22207112
National Natural Science Foundation of China (NSFC)China21977104

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release