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- PDB-3sw1: Structure of a full-length bacterial LOV protein -

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Basic information

Entry
Database: PDB / ID: 3sw1
TitleStructure of a full-length bacterial LOV protein
ComponentsSensory box protein
KeywordsSIGNALING PROTEIN / light-oxygen-voltage / LOV / PAS
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 / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain ...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 / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsGranzin, J. / Batra-Safferling, R. / Jaeger, K.-E. / Drepper, T. / Krauss, U.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Basis for the Slow Dark Recovery of a Full-Length LOV Protein from Pseudomonas putida.
Authors: Circolone, F. / Granzin, J. / Jentzsch, K. / Drepper, T. / Jaeger, K.E. / Willbold, D. / Krauss, U. / Batra-Safferling, R.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,1484
Polymers37,2362
Non-polymers9132
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-46 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.067, 55.067, 221.993
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:134 )
211chain B and (resseq 1:134 )

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Components

#1: Protein Sensory box protein / light-oxygen-voltage (LOV) photoreceptor


Mass: 18617.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP4629 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88E39
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM Tris, 8-18% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 6, 2010
Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry as the focusing system
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.63→55.5 Å / Num. all: 11307 / Num. obs: 11307 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 63.14 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.4
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.6 / Num. unique all: 506 / % possible all: 95.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_632)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N9L

1n9l


Resolution: 2.63→46.626 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 27.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 541 4.82 %RANDOM
Rwork0.2104 ---
all0.2118 11307 --
obs0.2118 11233 99.62 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.826 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso mean: 66.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.1026 Å20 Å2-0 Å2
2--2.1026 Å2-0 Å2
3----4.2053 Å2
Refinement stepCycle: LAST / Resolution: 2.63→46.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 62 15 2192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182209
X-RAY DIFFRACTIONf_angle_d1.3162986
X-RAY DIFFRACTIONf_dihedral_angle_d17.191900
X-RAY DIFFRACTIONf_chiral_restr0.109330
X-RAY DIFFRACTIONf_plane_restr0.005389
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1055X-RAY DIFFRACTIONPOSITIONAL
12B1055X-RAY DIFFRACTIONPOSITIONAL0.022
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6301-2.89480.37941130.31212684279799
2.8948-3.31350.27541530.245126462799100
3.3135-4.17430.231420.191426732815100
4.1743-46.63290.21151330.19392689282299

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