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- PDB-7r56: Crystal structure of PpSB1-LOV-I48T mutant (light state) -

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Basic information

Entry
Database: PDB / ID: 7r56
TitleCrystal structure of PpSB1-LOV-I48T mutant (light state)
ComponentsSensory box protein
KeywordsSIGNALING PROTEIN / LOV domain / PAS domain / Photocycle / 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 / 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 KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGranzin, J. / Batra-Safferling, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Photochem Photobiol Sci / Year: 2023
Title: Residue alterations within a conserved hydrophobic pocket influence light, oxygen, voltage photoreceptor dark recovery.
Authors: Hemmer, S. / Schulte, M. / Knieps-Grunhagen, E. / Granzin, J. / Willbold, D. / Jaeger, K.E. / Batra-Safferling, R. / Panwalkar, V. / Krauss, U.
History
DepositionFeb 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0622
Polymers18,6061
Non-polymers4561
Water00
1
A: Sensory box protein
hetero molecules

A: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1244
Polymers37,2122
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area5910 Å2
ΔGint-47 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.745, 54.745, 218.671
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Sensory box protein


Mass: 18605.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mutant: I48T / Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria)
Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / 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.: 1 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.085 M HEPES pH 7.5, 17 % (w/v) PEG 4000, 15 % (v/v) glycerol, 8.5 % (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 9, 2018
RadiationMonochromator: Si[111] monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.85→46.33 Å / Num. obs: 5076 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 113.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.025 / Rrim(I) all: 0.057 / Net I/σ(I): 14.4
Reflection shellResolution: 2.85→3 Å / Rmerge(I) obs: 1.037 / Num. unique obs: 702 / CC1/2: 0.838 / Rpim(I) all: 0.485 / Rrim(I) all: 1.148

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SW1

3sw1


Resolution: 2.85→46.33 Å / SU ML: 0.6192 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.3956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2735 480 9.55 %
Rwork0.231 4544 -
obs0.2354 5024 98.8 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.82 Å2
Refinement stepCycle: LAST / Resolution: 2.85→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 31 0 1136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031153
X-RAY DIFFRACTIONf_angle_d0.51891556
X-RAY DIFFRACTIONf_chiral_restr0.0399165
X-RAY DIFFRACTIONf_plane_restr0.0059206
X-RAY DIFFRACTIONf_dihedral_angle_d11.4497440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.070.371960.3549861X-RAY DIFFRACTION98.46
3.07-3.380.381960.3557865X-RAY DIFFRACTION98.97
3.38-3.870.3471960.2987901X-RAY DIFFRACTION99.8
3.87-4.870.326960.2284909X-RAY DIFFRACTION98.92
4.87-46.330.206960.18981008X-RAY DIFFRACTION97.96
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)
10.8947723020311.45480182835-1.456116472192.38470630743-2.436106422643.841062224770.7412844653650.354761164260.3697789825861.06375707966-0.07847111749740.913504731391-0.848012762469-0.869153760666-0.9953301310781.30832892015-0.2785462137370.1260572318371.300710390810.2100409660091.202532668133.7035714919942.844106451922.2293108012
23.44125246370.813797707083-0.5184362788274.751408072191.01272984017.074630353780.02361502896370.23743982225-0.312718031920.04596684508780.228670378077-0.4997559048481.26014791621.71384490114-0.3128906755731.02053990070.200756680893-0.03902031827141.35543311932-0.03667472390981.04801012582.381178030925.380375092113.0885405119
34.562688466713.41658075575-6.304942271472.72558659256-4.967618788839.07030308899-0.0214492089007-0.8606962502810.1839921378251.50739782781-0.980408654061-1.11976280152-0.7507499216313.097421698440.6887811952911.09536257320.396287143108-0.1593174736121.85164204643-0.06618616380831.464556927656.850830454515.026228386710.4501683476
41.208348120151.44278281556-0.4803148266482.64832855148-1.516434030551.05088323294-0.706494730006-0.276908064235-0.41695556987-1.037005536620.153832202617-0.5627840693251.341224012750.9278856828350.03937088895271.415352803440.02009586670960.0006254892517292.05610176033-0.3199510841521.09351731382-3.2727227595816.4061409051.72542724855
56.470558825750.9310409201460.2032954975653.075388172220.3230161134622.96227758044-0.03869173421810.774676467729-0.359463607243-1.046999280230.289608066810.150586271810.283838790051-1.13901278297-0.4167856539481.316776765370.0850536196511-0.05704983770641.50602756032-0.1666637894080.986313992315-10.433724882921.4617412064.51051913627
64.656962157123.66970391098-3.734431390954.57750573239-2.367044420764.863968570020.197763869819-1.09460307164-0.659649184162-1.37342545657-0.0615612799539-1.268863942110.40741349485-0.254086625648-0.0902775605061.104472424070.105427695818-0.1838374412291.257846140140.1047839228341.06683196147-7.9589754019225.05647233569.05658637678
79.012969319131.1588363081-5.201822743757.41350667031-5.155634375787.40599856016-1.692475511950.6053854107340.825416104584-4.355164924120.796906777876-0.1904824680312.34967006928-0.3785066050970.8768772694361.301721370430.082331085585-0.1306712515381.35957830842-0.06749839806850.719683934198-1.0389299809131.87696506977.36641166512
82.514737422080.04927757763373.377075437153.80379152849-0.9558206632285.962465428342.693077255760.295552275445-0.847252387994-0.100057461192-1.74564105445-0.1115959742631.57096151807-0.139154384108-0.709775172761.34908562903-0.155277130831-0.007524970523061.645223034640.03144920699681.37666206658-25.09805732312.862428463815.3075249017
98.60556181399-0.6681442704145.016596013214.96987238265-0.5812901328453.07081313801-0.7966077701750.31173844729-0.6623898544881.34335255173-1.353181867430.427134759818-0.375255314121-0.9834315045152.299624819681.094882483140.2921899691740.03289637512461.930393989080.1076333866841.12509909437-5.4053651366522.31449521623.02162992082
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 3 )A-2 - 31 - 6
22chain 'A' and (resid 4 through 41 )A4 - 417 - 44
33chain 'A' and (resid 42 through 48 )A42 - 4845 - 51
44chain 'A' and (resid 49 through 63 )A49 - 6352 - 66
55chain 'A' and (resid 64 through 91 )A64 - 9167 - 94
66chain 'A' and (resid 92 through 104 )A92 - 10495 - 107
77chain 'A' and (resid 105 through 119 )A105 - 119108 - 122
88chain 'A' and (resid 120 through 134 )A120 - 134123 - 137
99chain 'A' and (resid 500 through 500 )B500

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