3P84 | pdb_00003p84

Y351A mutant of pentaerythritol tetranitrate reductase containing a bound acetate molecule

PDB DOI: https://doi.org/10.2210/pdb3P84/pdb

Classification: OXIDOREDUCTASE
Organism(s): Enterobacter cloacae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-10-13 Released: 2011-04-06
Deposition Author(s): Toogood, H.S., Scrutton, N.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.140 (Depositor), 0.137 (DCC)
R-Value Work:
0.124 (Depositor), 0.121 (DCC)
R-Value Observed:
0.125 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Active site modifications in pentaerythritol tetranitrate reductase can lead to improved product enantiopurity, decreased by-product formation and altered stereochemical outcome in reactions with a,b-unsaturated nitroolefins

Fryszkowska, A., Toogood, H.S., Sakuma, M., Stephens, G.M., Gardiner, J.M., Scrutton, N.S.

(2011) Catalysis Science And Technology

Macromolecule Content

Total Structure Weight: 39.96 kDa
Atom Count: 3,507
Modeled Residue Count: 362
Deposited Residue Count: 365
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pentaerythritol tetranitrate reductase	A	365	Enterobacter cloacae	Mutation(s): 1 Gene Names: onr, PETNR EC: 1.6.99.1
UniProt
Find proteins for P71278 (Enterobacter cloacae) Explore P71278 Go to UniProtKB: P71278
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P71278
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.140 (Depositor), 0.137 (DCC)
R-Value Work: 0.124 (Depositor), 0.121 (DCC)
R-Value Observed: 0.125 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.427	α = 90
b = 70.329	β = 90
c = 88.876	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
d*TREK	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.