PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (2024)

EntryDatabase: PDB / ID: 7tta
TitleP450 (OxyA) from kistamicin biosynthesis, mixed heme conformation, attenuated beam
PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (1)ComponentsPutative cytochrome P450 hydroxylase
PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (2)KeywordsPDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (3)OXIDOREDUCTASE / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (4)Cytochrome P450 / peptide cyclase / NRPS-associated / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (5)glycopeptide antibiotic
Function / hom*ology

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (6)Function and hom*ology information

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (7)monooxygenase activity / iron ion binding / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (8)heme binding
Similarity search - Function

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (9)Cytochrome P450, B-class / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (10)Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (11)Cytochrome P450 / Cytochrome P450 superfamily / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (12)Cytochrome P450
Similarity search - Domain/hom*ology

PROTOPORPHYRIN IX CONTAINING FE / Putative cytochrome P450 hydroxylase
Similarity search - Component

Biological speciesPDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (13)Actinomadura parvosata subsp. kistnae (bacteria)
MethodPDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (14)X-RAY DIFFRACTION / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (15)SYNCHROTRON / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (16)MOLECULAR REPLACEMENT / Resolution: 2.001 Å
PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (17)AuthorsGreule, A. / Izore, T. / Cryle, M.J.
Funding support PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (18)Australia, PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (19)Germany, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1140619 PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (20)Australia
Australian Research Council (ARC)DP170102220 PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (21)Australia
German Research Foundation (DFG)CR 392/1-1 PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (22)Germany
PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (23)CitationJournal: Front Chem / Year: 2022
Title: The Cytochrome P450 OxyA from the Kistamicin Biosynthesis Cyclization Cascade is Highly Sensitive to Oxidative Damage.
Authors: Greule, A. / Izore, T. / Machell, D. / Hansen, M.H. / Schoppet, M. / De Voss, J.J. / Charkoudian, L.K. / Schittenhelm, R.B. / Harmer, J.R. / Cryle, M.J.
History
DepositionFeb 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Deposited unit

A: Putative cytochrome P450 hydroxylase

hetero molecules


PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (25)

  • 43.1 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)43,0883
Polymers42,3801
Non-polymers7092
Water4,125229
1
  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-26 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.051, 70.051, 132.668
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
#1: Protein Putative cytochrome P450 hydroxylase

Mass: 42379.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (27)Actinomadura parvosata subsp. kistnae (bacteria)
Gene: KIS93_04812 / Production host: PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (28)PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (29)PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (30)Escherichia coli BL21 (bacteria) / Strain (production host): ArcticExpress / References: UniProt: A0A2P9IBF7

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (31)

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (32)

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (33)

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (34)

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (35)Glycerol

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (37)

Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (38)

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (39)

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (40)Heme B

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (42)

Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (43)

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (44)

#4: Water ChemComp-HOH / water / PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (45)Water

Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

PDB-7tta: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation... (47)

Has ligand of interestY

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