8A36 | pdb_00008a36

Crystal structure of PpSB1-LOV-K117E mutant (dark state), monoclinic form

PDB DOI: https://doi.org/10.2210/pdb8A36/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.
Funding Organization(s): German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.272 (Depositor), 0.270 (DCC)
R-Value Work:
0.225 (Depositor), 0.220 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of PpSB1-LOV-K117E mutant (dark state), monoclinic form

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

To be published.

Macromolecule Content

Total Structure Weight: 76.3 kDa
Atom Count: 4,431
Modeled Residue Count: 531
Deposited Residue Count: 648
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, B, C, D	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
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.272 (Depositor), 0.270 (DCC)
R-Value Work: 0.225 (Depositor), 0.220 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.754	α = 90
b = 80.929	β = 93.846
c = 94.37	γ = 90

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: 2023-07-19
Changes: Refinement description
Version 1.2: 2024-02-07
Changes: Data collection, Refinement description

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.