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- PDB-7r5n: Crystal structure of the full-length short LOV protein PF5-LOV fr... -

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Basic information

Entry
Database: PDB / ID: 7r5n
TitleCrystal structure of the full-length short LOV protein PF5-LOV from Pseudomonas fluorescens (dark state)
ComponentsSensory box protein
KeywordsSIGNALING PROTEIN / LOV domain / short LOV / PAS domain / Photocycle / Dimerization / Signaling blue light photoreceptor
Function / homology
Function and homology information


PAS domain / PAS-associated, C-terminal / PAC domain profile. / 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 / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsArinkin, V. / Batra-Safferling, R. / Granzin, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Conserved Signal Transduction Mechanisms and Dark Recovery Kinetic Tuning in the Pseudomonadaceae Short Light, Oxygen, Voltage (LOV) Protein Family.
Authors: Arinkin, V. / Granzin, J. / Jaeger, K.E. / Willbold, D. / Krauss, U. / Batra-Safferling, R.
History
DepositionFeb 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)39,8144
Polymers38,9012
Non-polymers9132
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-48 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.698, 148.698, 200.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 1 through 149 or resid 500))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 149
211(chain B and (resid 1 through 149 or resid 500))B0

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Components

#1: Protein Sensory box protein


Mass: 19450.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: PFL_0954
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q4KI48
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
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: 7.13 Å3/Da / Density % sol: 82.76 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / Details: 1.2 M (NH4)2SO4, 0.1M MES / PH range: 6.0 - 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.45→48.12 Å / Num. obs: 15076 / % possible obs: 99.5 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.041 / Rrim(I) all: 0.091 / Net I/σ(I): 9
Reflection shellResolution: 3.45→3.78 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3526 / CC1/2: 0.531 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J3W

5j3w


Resolution: 3.45→48.12 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 731 4.88 %
Rwork0.2152 14256 -
obs0.2168 14987 98.81 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 322.82 Å2 / Biso mean: 195.6399 Å2 / Biso min: 131.26 Å2
Refinement stepCycle: final / Resolution: 3.45→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 62 0 2460
Biso mean--194.76 --
Num. residues----300
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1356X-RAY DIFFRACTION14.421TORSIONAL
12B1356X-RAY DIFFRACTION14.421TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.45-3.720.34281380.32652756289497
3.72-4.090.35131750.31322765294099
4.09-4.680.31451450.23582840298599
4.68-5.90.23991250.23862884300999
5.9-48.120.21241480.17963011315999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4269-1.14770.53762.754-1.90040.9385-0.02721.3776-1.5529-0.5281-0.1967-1.90222.5924-0.2673-0.00392.50670.1462-0.2071.49620.15891.936-43.297443.367916.3774
210.6411-1.0566-3.72753.6239-3.21373.95240.52680.2515-0.90060.3582-0.20360.29310.4080.2519-0.00212.5401-0.1127-0.12291.78440.12551.8381-57.323331.380615.037
34.4891-2.3503-1.89652.67540.17414.4593-0.46461.1833-0.6153-0.14070.06441.3790.9870.146-0.00242.5694-0.3272-0.21461.77880.07852.285-65.633128.12765.7881
42.2289-3.19752.09255.15350.69834.7074-0.3742-1.0581-0.96450.22690.84741.4857-0.42480.5629-0.00131.9612-0.0654-0.04771.8774-0.04731.9479-67.482336.150511.4051
5-0.0508-0.1302-0.08340.52280.13940.0391-1.00790.21170.938-2.21390.5416-3.09121.90853.02870.00192.22140.42920.3182.5019-0.393.1975-45.538830.03-2.9987
61.16240.9237-0.2561.9446-1.34541.3477-2.06253.4883-1.08671.64570.20441.16411.5442-2.1814-0.0111.8565-0.18190.15791.825-0.20991.9234-59.293937.10439.0334
71.119-4.25553.4770.5708-1.9896-2.33911.47051.3587-1.5441-2.0554-0.96142.1251.2130.13890.00132.38610.1012-0.12862.24010.16692.9451-89.055654.10587.3653
80.1892-0.25480.2641.4975-0.59480.2808-0.71440.0403-1.03473.57633.7433.07093.66270.29970.02492.81060.0776-0.51591.7298-0.16571.7747-64.280828.86847.5277
98.51131.2690.940510.9635-4.13610.33170.0312-0.04660.5768-0.69070.0559-0.3365-0.55440.6790.00022.0635-0.0750.16811.84990.02461.7484-45.37147.739312.3737
108.1143-2.56540.39792.871-0.60628.84690.0853-0.07651.1240.35290.17030.2724-0.93070.3129-0.00032.3149-0.23640.20871.71280.00121.8923-53.36360.572214.0228
110.82951.0322-0.33230.407-0.39850.3873-1.5357-3.9041-0.24133.2285-0.5983-3.06230.76113.3782-0.00182.4759-0.0878-0.52733.00990.28212.5803-38.887349.379526.8902
123.01241.27461.7652-0.9423-0.6039-0.9324-0.9097-1.69671.63190.43040.8111-0.0515-0.3088-0.33240.00042.19770.13710.09872.44280.06242.438-81.196559.882111.5602
130.1294-0.0599-0.1840.33760.29310.1427-1.85582.6908-0.4448-2.84280.0576-0.46391.45591.3432-0.00212.7879-0.95510.55422.5914-0.45731.8682-50.608362.227817.3791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )A1 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 47 )A14 - 47
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 78 )A48 - 78
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 102 )A79 - 102
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 110 )A103 - 110
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 119 )A111 - 119
7X-RAY DIFFRACTION7chain 'A' and (resid 120 through 149 )A120 - 149
8X-RAY DIFFRACTION8chain 'A' and (resid 500 through 500 )A500
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 33 )B1 - 33
10X-RAY DIFFRACTION10chain 'B' and (resid 34 through 101 )B34 - 101
11X-RAY DIFFRACTION11chain 'B' and (resid 102 through 111 )B102 - 111
12X-RAY DIFFRACTION12chain 'B' and (resid 112 through 151 )B112 - 151
13X-RAY DIFFRACTION13chain 'B' and (resid 500 through 500 )B500

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