5FYG

Structure of CYP153A from Marinobacter aquaeolei in complex with hydroxydodecanoic acid

PDB DOI: https://doi.org/10.2210/pdb5FYG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Marinobacter nauticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-03-07 Released: 2017-01-18
Deposition Author(s): Danesh-Azari, H.-R., Spandolf, C., Hoffman, S.M., Weissenborn, M., Hauer, B., Grogan, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 ?
R-Value Free: 0.239
R-Value Work: 0.187
R-Value Observed: 0.190

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure-Guided Redesign of CYP153AM.aqfor the Improved Terminal Hydroxylation of Fatty Acids

Hoffman, S.M., Danesh Azari, H.-R., Spandolf, C., Weissenborn, M., Grogan, G., Hauer, B.

(2016) ChemCatChem

DOI: https://doi.org/10.1002/cctc.201600680

Macromolecule Content

Total Structure Weight: 109.7 kDa
Atom Count: 7,014
Modelled Residue Count: 841
Deposited Residue Count: 940
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450	A, B	470	Marinobacter nauticus	Mutation(s): 0
UniProt
Find proteins for A1TY82 (Marinobacter nauticus (strain ATCC 700491 / DSM 11845 / VT8)) Explore A1TY82 Go to UniProtKB: A1TY82
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1TY82
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
12H Query on 12H Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	12-HYDROXYDODECANOIC ACID C₁₂ H₂₄ O₃ ZDHCZVWCTKTBRY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 ?
R-Value Free: 0.239
R-Value Work: 0.187
R-Value Observed: 0.190
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 59.02	α = 90
b = 71.31	β = 90
c = 213.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-01-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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5FYG

Structure of CYP153A from Marinobacter aquaeolei in complex with hydroxydodecanoic acid

Structure-Guided Redesign of CYP153AM.aqfor the Improved Terminal Hydroxylation of Fatty Acids

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)