4AWS | pdb_00004aws

Crystal structure of the oxidized Shewanella Yellow Enzyme 1 (SYE1) M25L mutant

PDB DOI: https://doi.org/10.2210/pdb4AWS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Shewanella oneidensis MR-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-06-05 Released: 2013-06-26
Deposition Author(s): Elegheert, J., Brige, A., Savvides, S.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.135 (Depositor), 0.136 (DCC)
R-Value Work:
0.124 (DCC)
R-Value Observed:
0.116 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Modulation of Isoalloxazine Ring Planarity Influences Fmn Electronic Properties in Old Yellow Enzymes

Elegheert, J., Pauwels, E., Wille, G., Brige, A., Savvides, S.N.

To be published.

Macromolecule Content

Total Structure Weight: 41.28 kDa
Atom Count: 3,662
Modeled Residue Count: 364
Deposited Residue Count: 365
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYE1	A	365	Shewanella oneidensis MR-1	Mutation(s): 1 EC: 1.6.99.1
UniProt
Find proteins for Q8EEC8 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EEC8 Go to UniProtKB: Q8EEC8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8EEC8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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]
PE4 Query on PE4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
BOG Query on BOG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
01F Query on 01F 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]	ethyl hydrogen carbonate C₃ H₆ O₃ CQDGTJPVBWZJAZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.135 (Depositor), 0.136 (DCC)
R-Value Work: 0.124 (DCC)
R-Value Observed: 0.116 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.56	α = 90
b = 83.9	β = 90
c = 87.76	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-26

Deposition Author(s):

Elegheert, J.

Brige, A.

Savvides, S.N.

Revision History (Full details and data files)

Version 1.0: 2013-06-26
Type: Initial release
Version 1.1: 2019-05-22
Changes: Data collection, Derived calculations, Other, Refinement description
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-10-09
Changes: Structure summary