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- PDB-5j3w: Crystal structures reveal signaling states of a short blue light ... -

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Basic information

Entry
Database: PDB / ID: 5j3w
TitleCrystal structures reveal signaling states of a short blue light photoreceptor protein PpSB1-LOV (dark state)
ComponentsSensory box protein
KeywordsSIGNALING PROTEIN / LOV domain / PAS domain
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 / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain ...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 / 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: 2.55 Å
AuthorsGranzin, J. / Batra-Safferling, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Bundesministerium fuer Bildung und ForschungFKZ-031A167B Germany
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Signaling States of a Short Blue-Light Photoreceptor Protein PpSB1-LOV Revealed from Crystal Structures and Solution NMR Spectroscopy.
Authors: Rollen, K. / Granzin, J. / Panwalkar, V. / Arinkin, V. / Rani, R. / Hartmann, R. / Krauss, U. / Jaeger, K.E. / Willbold, D. / Batra-Safferling, R.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Sensory box protein
D: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2978
Polymers74,4714
Non-polymers1,8254
Water00
1
A: Sensory box protein
C: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1484
Polymers37,2362
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-42 kcal/mol
Surface area13590 Å2
MethodPISA
2
B: Sensory box protein
D: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1484
Polymers37,2362
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-38 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.379, 71.086, 91.264
Angle α, β, γ (deg.)90.00, 91.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Sensory box protein


Mass: 18617.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain KT2440) (bacteria)
Strain: KT2440 / Gene: PP_4629 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88E39
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P

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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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Na-cacodylate, MgCl2, PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2014
RadiationMonochromator: Silicon (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.55→45.001 Å / Num. obs: 21326 / % possible obs: 99.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 14.7
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 1.5 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SW1

3sw1


Resolution: 2.55→45.001 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.2
RfactorNum. reflection% reflection
Rfree0.2546 1071 5.11 %
Rwork0.1915 --
obs0.1947 20946 97.31 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.55→45.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 124 0 4194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114256
X-RAY DIFFRACTIONf_angle_d1.4995779
X-RAY DIFFRACTIONf_dihedral_angle_d17.3141516
X-RAY DIFFRACTIONf_chiral_restr0.065642
X-RAY DIFFRACTIONf_plane_restr0.008744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.66610.42561170.30622188X-RAY DIFFRACTION87
2.6661-2.80660.34811430.27412465X-RAY DIFFRACTION98
2.8066-2.98240.3571310.26982543X-RAY DIFFRACTION99
2.9824-3.21260.37461450.26052499X-RAY DIFFRACTION99
3.2126-3.53580.34521200.22612529X-RAY DIFFRACTION99
3.5358-4.04720.26251550.19822509X-RAY DIFFRACTION99
4.0472-5.09790.20321270.15782565X-RAY DIFFRACTION99
5.0979-45.00820.20161330.16482577X-RAY DIFFRACTION98
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)
13.9310.35960.84621.0237-0.02353.8719-0.4004-0.9862-0.07740.0850.07040.0152-0.23020.44530.29640.78410.2174-0.04240.98290.03310.68724.1703-0.621923.1644
27.08180.4122-2.0255.92324.98925.8919-0.1465-2.1794-0.46251.4137-0.2829-0.2037-1.77280.85860.35421.36730.0896-0.11361.2436-0.06380.720412.09170.720532.699
37.3467-1.9754-0.6915.9657-1.21173.1286-0.3744-0.6909-0.81190.76110.1141-1.34020.56940.72690.25350.9350.1745-0.02321.17970.17470.957219.8865-11.653525.4668
43.8452-0.66070.56856.06010.59135.0938-0.4206-1.44770.20621.12790.2516-0.01590.00230.87340.48520.9690.19160.1281.04540.15980.673912.386-8.450930.8408
52.20991.354-0.92456.48560.17756.3409-0.2097-0.09520.23010.42430.90190.4767-1.1725-0.5427-0.50130.44140.13110.02391.00590.09920.58919.1075-3.365718.426
62.9501-0.98843.34113.7505-2.63364.5134-1.5985-1.5411-2.0317-0.8207-0.2-1.5461.56210.06420.9891.56330.270.50611.50510.99921.390412.4433-25.674441.1332
74.04012.1088-5.81737.2208-0.46059.53140.2111-0.81170.0391.1848-1.30880.2005-0.66440.64481.08691.22140.32070.00281.196-0.18131.256818.3331-5.901426.2264
87.4189-2.1597-0.80266.7691-2.36519.23810.02481.62280.78540.5337-0.00210.7314-0.4274-0.04570.36640.5740.08970.06810.74060.08350.758715.6968-28.17850.6388
99.9782-0.1301-7.11633.57522.53328.14740.0853-2.07241.0109-0.24570.7506-0.3317-0.1661.6464-0.89220.7460.0027-0.12260.7835-0.17180.679933.7697-24.39490.7394
108.41352.0196-3.72186.4818-0.21026.71320.39561.39261.1094-0.9557-0.03161.1624-1.5179-1.0622-0.43710.99970.1347-0.02180.70710.08620.939729.2255-14.62895.0629
112.8924-1.966-0.73145.2248-1.70374.61270.25420.67240.72830.4806-0.257-1.043-0.18931.17710.11170.74990.0468-0.02011.11640.06781.300943.2598-24.00967.3536
127.6751-0.69650.62228.0062-0.08927.5828-0.288-1.5905-0.76190.44240.14370.05240.59680.61880.16560.51420.1658-0.04020.9408-0.02180.857639.5611-28.913911.6974
134.1709-0.90811.1334.4614-1.42335.5184-0.138-0.94990.07190.16950.0137-0.8015-0.7827-0.53320.16720.83120.3147-0.07930.8731-0.10850.923534.9159-22.671310.9446
142.28590.87750.04263.58941.90125.8685-0.2336-0.40740.2442-0.24510.4623-0.3443-0.31630.1787-0.12950.39580.0534-0.06070.6871-0.11430.638631.9615-30.5151-0.1634
152.95040.03312.24291.43780.4321.8131-0.7945-2.6937-0.28052.1465-1.3038-1.12740.092-0.05951.42721.86060.2969-0.15821.96580.04881.00934.2342-21.279432.1567
162.6051-0.3273-1.95771.8021-0.98162.32521.0347-1.34361.0024-0.16530.46741.6806-0.6980.864-1.11010.85540.180.08571.73580.09561.736340.6695-24.75576.1195
174.10640.1152-0.95356.2669-1.37355.0677-0.355-0.6137-0.00550.05830.2793-0.2299-0.0802-0.30030.02490.81550.1717-0.00741.08870.04840.8043-4.0828-5.686621.0346
183.0520.6415-0.76317.5798-1.42150.6839-0.137-2.6808-0.7134-0.9735-0.24830.68070.2654-1.39770.47830.65720.0978-0.00761.5660.11581.0942-11.9849-15.814520.4162
190.9580.2952-0.54010.1447-0.12590.13660.2053-0.5955-1.7984-0.8722-2.66290.8017-0.10960.27441.17062.21930.7639-0.09013.11450.56470.873-18.1408-20.535527.3373
201.7266-2.3381-1.2474.50721.75712.0978-0.7357-1.4012-0.71471.4184-0.02421.40250.3607-1.10080.69221.12150.28740.32732.25560.23741.1946-15.207-14.388337.1079
215.188-1.50131.18424.8975-1.20033.8625-0.2213-1.5802-1.69890.5441-0.45240.74930.2715-0.77820.44550.94990.27620.14421.30650.45421.0727-8.6977-19.644529.9601
222.20941.03411.63664.1822-2.00563.6043-0.30550.3431-0.3995-2.4711-0.92882.842-0.91-1.57691.20291.46840.5439-0.14621.59180.05311.5364-17.37493.663925.8365
234.9198-2.33570.10128.49840.99852.9234-0.1794-1.7665-0.3014-0.38630.40650.91170.3663-1.2695-0.27390.94770.12920.1771.40470.01120.8693-8.3749-11.493729.654
246.0381.0584-1.56193.87211.90241.74610.456-0.1887-0.87511.91690.50671.23512.1392-0.1428-0.18571.5910.45820.23781.60050.54821.23543.7364-29.5741.8852
252.5041.165-3.21073.7369-0.11284.7232-0.0127-0.527-1.3224-1.0727-0.32670.67790.0818-1.10540.40371.3107-0.0831-0.03361.59560.17011.4122-16.5992-15.664631.0338
266.9662-0.61181.00227.53240.36853.6882-0.4330.0234-0.17950.03350.8734-0.2984-0.1296-0.6209-0.32890.49410.0278-0.10910.6804-0.08770.78724.1923-32.0169-1.0179
273.7026-1.71652.59112.7246-0.43724.35870.0682-0.5447-1.3421-0.07160.12980.17130.898-0.2913-0.27730.81640.0387-0.01530.51440.16750.907110.6834-37.150313.04
283.25990.71551.43042.85741.60754.9804-0.1638-0.4894-0.20930.49910.09050.25220.24460.04190.06780.62740.13320.06770.66740.16940.72769.1333-27.869416.5036
291.96510.35710.37884.05862.26023.45060.3537-0.1478-0.21543.6735-0.0397-1.51050.3830.31-0.24811.67770.0455-0.30481.44460.3010.940225.2552-23.3235.4031
306.44342.5558-4.31931.71660.47969.39742.155-0.3841-0.30910.5864-0.64690.66810.222-0.2472-1.39910.86690.135-0.07430.5382-0.06430.87776.1171-30.601917.7519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 119 )
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 133 )
7X-RAY DIFFRACTION7chain 'A' and (resid 500 through 500 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 13 )
9X-RAY DIFFRACTION9chain 'B' and (resid 14 through 33 )
10X-RAY DIFFRACTION10chain 'B' and (resid 34 through 48 )
11X-RAY DIFFRACTION11chain 'B' and (resid 49 through 74 )
12X-RAY DIFFRACTION12chain 'B' and (resid 75 through 86 )
13X-RAY DIFFRACTION13chain 'B' and (resid 87 through 103 )
14X-RAY DIFFRACTION14chain 'B' and (resid 104 through 119 )
15X-RAY DIFFRACTION15chain 'B' and (resid 120 through 134 )
16X-RAY DIFFRACTION16chain 'B' and (resid 500 through 500 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 24 )
18X-RAY DIFFRACTION18chain 'C' and (resid 25 through 48 )
19X-RAY DIFFRACTION19chain 'C' and (resid 49 through 63 )
20X-RAY DIFFRACTION20chain 'C' and (resid 64 through 86 )
21X-RAY DIFFRACTION21chain 'C' and (resid 87 through 102 )
22X-RAY DIFFRACTION22chain 'C' and (resid 103 through 110 )
23X-RAY DIFFRACTION23chain 'C' and (resid 111 through 119 )
24X-RAY DIFFRACTION24chain 'C' and (resid 120 through 134 )
25X-RAY DIFFRACTION25chain 'C' and (resid 500 through 500 )
26X-RAY DIFFRACTION26chain 'D' and (resid 1 through 13 )
27X-RAY DIFFRACTION27chain 'D' and (resid 14 through 57 )
28X-RAY DIFFRACTION28chain 'D' and (resid 58 through 119 )
29X-RAY DIFFRACTION29chain 'D' and (resid 120 through 134 )
30X-RAY DIFFRACTION30chain 'D' and (resid 500 through 500 )

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