8A33 | pdb_00008a33

Crystal structure of PpSB1-LOV-K117E mutant (light state)

PDB DOI: https://doi.org/10.2210/pdb8A33/pdb

Classification: SIGNALING PROTEIN
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2022-06-07 Released: 2023-07-05
Deposition Author(s): Batra-Safferling, R., Granzin, J., Krauss, U.
Funding Organization(s): German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.288 (Depositor), 0.280 (DCC)
R-Value Work:
0.232 (Depositor), 0.230 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of PpSB1-LOV-K117E mutant (light state)

Batra-Safferling, R., Granzin, J., Krauss, U.

To be published.

Macromolecule Content

Total Structure Weight: 19.08 kDa
Atom Count: 1,112
Modeled Residue Count: 133
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensory box protein	A	162	Pseudomonas putida KT2440	Mutation(s): 1 Gene Names: PP_4629
UniProt
Find proteins for Q88E39 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88E39 Go to UniProtKB: Q88E39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q88E39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JGC (Subject of Investigation/LOI) Query on JGC 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 (semi-quinone intermediate) C₁₇ H₂₃ N₄ O₉ P JNFNEOXSUODPSY-DGAVXFQQSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.288 (Depositor), 0.280 (DCC)
R-Value Work: 0.232 (Depositor), 0.230 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.329	α = 90
b = 54.329	β = 90
c = 220.555	γ = 120

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Batra-Safferling, R.

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	FKZ 031A16

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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.