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- PDB-7a6p: Structural determinants underlying the adduct lifetime in a short... -

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Basic information

Entry
Database: PDB / ID: 7a6p
TitleStructural determinants underlying the adduct lifetime in a short LOV protein PpSB2-LOV
ComponentsPutative Sensory box protein
KeywordsSIGNALING PROTEIN / LOV domain / PAS domain / Dimerization / Signaling blue light photoreceptor
Function / homology
Function and homology information


PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsArinkin, V. / Granzin, J. / Batra-Safferling, R.
CitationJournal: Febs J. / Year: 2021
Title: Structural determinants underlying the adduct lifetime in the LOV proteins of Pseudomonas putida.
Authors: Arinkin, V. / Granzin, J. / Krauss, U. / Jaeger, K.E. / Willbold, D. / Batra-Safferling, R.
History
DepositionAug 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Sensory box protein
B: Putative Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5466
Polymers38,4212
Non-polymers1,1254
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-36 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.142, 88.467, 54.180
Angle α, β, γ (deg.)90.000, 106.030, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Putative Sensory box protein


Mass: 19210.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: PP_2739 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88JB0
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.6 % / Description: needle
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: Sodium acetate, polyethylene glycol 200, polyethylene glycol 3350
PH range: 4.9 - 5.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.93→44.88 Å / Num. obs: 25353 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.053 / Rrim(I) all: 0.111 / Net I/σ(I): 8.9 / Num. measured all: 107111
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) all% possible allRrim(I) all
1.93-1.9840.8917050.450.508100
9.05-44.884.20.0392590.9970.02299.60.045

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SW1

3sw1


Resolution: 1.93→44.88 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1944 1208 4.77 %
Rwork0.1769 --
obs0.1777 25325 99.94 %
Displacement parametersBiso mean: 39.18 Å2
Refinement stepCycle: LAST / Resolution: 1.93→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 73 82 2492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812493
X-RAY DIFFRACTIONf_angle_d0.90553394
X-RAY DIFFRACTIONf_chiral_restr0.0559369
X-RAY DIFFRACTIONf_plane_restr0.0064449
X-RAY DIFFRACTIONf_dihedral_angle_d21.1497931

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