2FEU

P450CAM from Pseudomonas putida reconstituted with manganic protoporphyrin IX

PDB DOI: https://doi.org/10.2210/pdb2FEU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-12-16 Released: 2006-03-14
Deposition Author(s): von Koenig, K., Makris, T.M., Sligar, S.G., Schlichting, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.238
R-Value Work: 0.214
R-Value Observed: 0.214

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The status of high-valent metal oxo complexes in the P450 cytochromes.

Makris, T.M., von Koenig, K., Schlichting, I., Sligar, S.G.

(2006) J Inorg Biochem 100: 507-518

PubMed: 16510191 Search on PubMed
DOI: https://doi.org/10.1016/j.jinorgbio.2006.01.025
Primary Citation of Related Structures:
2FE6, 2FER, 2FEU

PubMed Abstract:
The oxidative prowess of the P450 cytochromes in physiological reactions is attributed to the production of a high-valent iron-oxo complex, or Compound I intermediate, in the reaction cycle. Despite many years of study, however, the full electronic description of this fleeting intermediate still remains an active area of study. In this manuscript, the current status of the isolation and characterization of the P450 oxo-Fe(IV) is examined and compared to analogous states in related heme enzymes. In addition, the utilization of cofactor exchange to stabilize high-valent oxo-states in the P450 is addressed. Structural and spectroscopic studies on manganese reconstituted P450, and its corresponding oxo-complex, are presented.

Organizational Affiliation

Department of Biochemistry, University of Illinois Urbana-Champaign, 116 Morrill Hall, Urbana, IL 61801, USA. [email protected]

Macromolecule Content

Total Structure Weight: 94.72 kDa
Atom Count: 7,252
Modelled Residue Count: 809
Deposited Residue Count: 822
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-cam	A, B	411	Pseudomonas putida	Mutation(s): 0 Gene Names: camC, cyp101 EC: 1.14.15.1
UniProt
Find proteins for P00183 (Pseudomonas putida) Explore P00183 Go to UniProtKB: P00183
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00183
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MNR Query on MNR Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	PROTOPORPHYRIN IX CONTAINING MN C₃₄ H₃₂ Mn N₄ O₄ UAPHVASSHGRKEN-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
CAM Query on CAM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	CAMPHOR C₁₀ H₁₆ O DSSYKIVIOFKYAU-XCBNKYQSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], G [auth B], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.238
R-Value Work: 0.214
R-Value Observed: 0.214
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.13	α = 90
b = 62.23	β = 90.64
c = 94.71	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-03-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-03-14
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description