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- PDB-7r4s: Crystal structure of PpSB1-LOV-I48T mutant (dark state) -

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Basic information

Entry
Database: PDB / ID: 7r4s
TitleCrystal structure of PpSB1-LOV-I48T mutant (dark 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 / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 9, 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
B: Sensory box protein
C: Sensory box protein
D: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2488
Polymers74,4234
Non-polymers1,8254
Water00
1
A: Sensory box protein
B: 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
Buried area5070 Å2
ΔGint-35 kcal/mol
Surface area13540 Å2
2
C: Sensory box protein
D: 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
Buried area5210 Å2
ΔGint-41 kcal/mol
Surface area13780 Å2
Unit cell
Length a, b, c (Å)101.416, 72.146, 91.715
Angle α, β, γ (deg.)90.000, 90.178, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Sensory box protein


Mass: 18605.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: mutation: 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.: 4 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M sodium chloride, 0.1 M MES pH 6.0, 15 % (v/v) pentaerythritol propoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2018
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.75→45.86 Å / Num. obs: 17276 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 72 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.082 / Rrim(I) all: 0.192 / Net I/σ(I): 3.4
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2502 / CC1/2: 0.705 / Rpim(I) all: 0.445 / Rrim(I) all: 0.999 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MxCuBE3data collection
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J3W

5j3w


Resolution: 2.75→36.19 Å / SU ML: 0.4443 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.0905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2785 798 4.67 %
Rwork0.2289 16282 -
obs0.2313 17080 98.25 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.48 Å2
Refinement stepCycle: LAST / Resolution: 2.75→36.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4292 0 124 0 4416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00114481
X-RAY DIFFRACTIONf_angle_d0.30586051
X-RAY DIFFRACTIONf_chiral_restr0.0365641
X-RAY DIFFRACTIONf_plane_restr0.0025788
X-RAY DIFFRACTIONf_dihedral_angle_d13.38461699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.920.43891250.34262640X-RAY DIFFRACTION96.01
2.92-3.150.37281370.33942677X-RAY DIFFRACTION97.74
3.15-3.460.33821140.2842724X-RAY DIFFRACTION98.47
3.46-3.970.32231190.2562748X-RAY DIFFRACTION99.2
3.97-4.990.2491530.20832708X-RAY DIFFRACTION99.24
5-36.190.24041500.18422785X-RAY DIFFRACTION98.82
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)
13.406771097521.331971521692.472743747383.506097565290.9868157952464.322157077560.0351020139551-0.05893608063020.649053316768-0.01550418376050.09791497974220.0471751985965-0.2594688627730.236039936228-0.2878584088490.6775088488420.13306773465-0.05488401924630.7115499469830.03922162489810.83403989841730.07982775787.06245338442.32711460926
23.93512123905-0.3382725327881.684780430518.67264490715-0.2368452326714.081194732390.194151021264-1.10302578772-0.467962430622-0.346747436455-0.314979527209-1.81300987561-0.004247592590010.4979408109870.1282197378270.8146303505420.160593060610.07592572409171.26984378470.05192311306471.2595151854843.14167000380.18858371714910.9842129493
31.15691683599-0.144100113931-1.220200204892.561579644771.620500001654.63710070617-0.273032785659-0.6150328998310.368431856610.4953843287560.609637124227-0.5247301996350.435441764749-0.481455068467-0.4832413550020.5191771125010.245537072832-0.005216657734420.763439029989-0.1053641377950.95636678950933.27874662511.698066208335.55547977559
46.962737825885.661425977172.842225666966.647608758380.5624657651212.762999875452.194061443910.373888738556-0.772512996222-0.116104428694-2.44884855742-1.754155741791.10090241245-1.80475243914-0.7616664953721.666792990090.442756460955-0.2906534669861.40514355474-0.2310187101071.2095497827933.7279488977.8029472805330.8798938463
50.19858537471.00505567924-0.3870623936976.01017633704-1.882988949370.8581311394262.40961071556-4.147670564443.060099231210.800697441992-2.4832799604-1.88726724678-0.693940089921-1.65337824565-0.1154363383681.00480874625-0.209424626847-0.2045309027841.44100392908-0.2164003926081.2277413398540.59520366783.478446501286.20509404985
64.982338004540.1930150589190.5686053848442.737155097561.815449366363.690173259460.544399695816-0.195115147543-0.869103476789-0.174373956894-0.276165573912-0.2239232091220.1104168492190.73416015223-0.1594605497550.718524438430.11288673917-0.1186854510890.6338295581850.00450149900570.78546508846614.579977899-4.741707663765.98742070187
74.823559837063.01242370279-1.320588863542.7108414532-1.354979765594.66649596186-0.809506698692-0.71510220492-0.977388482510.0100273193466-0.298564884327-0.7081560230220.7379035988520.35474362713-0.1597868553280.5920323563211.67305815464-0.231107430663-0.0586878333993-0.2412224872120.86338803915919.269235381-10.400865857915.0015039699
83.19192776781-0.9345468270630.8771347125185.75550842567-2.513014652724.97556180687-0.378820731205-0.455484096164-0.7940714302940.9399728528180.2108089794250.07985683391451.554703921450.3826880580610.4159593044811.080847213160.07034929438210.02481140514530.960536843410.1504319838690.8849363277977.55294080792-9.0394372132319.4194851622
97.97902687632-0.4528741937792.36682466962.98168863033-0.07928010505826.2363478996-0.81890942812-0.2684180385791.41636878361.09479402543-0.03527879474160.714413433744-0.598369079316-0.5519549431840.336615642930.7046311531180.1061240156460.1269162221780.3437288856470.11184315530.664475016452.493343162725.5524889043818.1323989891
105.56780465241-1.58198702561-0.1658342685773.159667912922.619276517584.64699652548-0.669738374249-1.038532719510.257580710041.083882047060.756429710084-0.454916908882-0.9989871062880.1447147780550.01981851088460.8422982715320.1111914954780.08915828215570.847649593119-0.02564654902990.793664287229.766299114044.2308985152819.5180791595
111.10901038691-0.0715126645070.5098572445662.085556658932.898676921674.65528955402-0.346988417496-0.357608170650.2190133820480.7435997795920.332599386517-0.2241920908560.821529198415-0.357226600836-0.03699240165040.7314507228820.164847463433-0.05479394599070.7081323363020.01201140648980.82093815060913.6394856228-2.4001551239418.1469370078
121.85326284909-0.1629442280331.229662603031.721898085950.06563578531532.964807088670.202321553173-0.00902870076051-0.4497148087040.06473134500710.0322261243463-0.1375543545251.15490964490.330797982768-0.2626561842890.7372250307510.1280557137580.09414488374850.527149843665-0.0029536152090.7142195283519.86695198271-0.1135429839576.42350303266
133.772006382853.475433667994.120638841976.004831993734.559826641964.763145905450.9056450102440.967231203828-1.406754844981.717921959930.320444201423-1.600315151732.028170327723.18356380326-1.211966557311.578462329970.122114017517-0.1825731823931.089983615110.1282775983680.84360402851225.46272799064.8962676788434.5640420796
142.40071313457-1.16887387896-0.8590342018272.20516883764-1.371813798682.253579538610.803606152255-1.16364945083-1.947904949741.33595858576-1.297357507940.3942590079242.407537354981.174313716890.8306831702721.34491521671-0.0976897310972-0.1413639156311.12946056844-0.04953203146421.075373903056.22503083115-2.0072209429417.6826462998
158.797089000810.142279226849-4.013651758435.87245824192-3.885351089534.44676445879-0.9137373944280.04646388554970.345037385585-2.273681396571.03218218997-1.055232116191.126666910070.07543611171630.481085935531.007701760370.0155010249833-0.08705221253080.92474338551-0.01624267813340.819973706241.2538221906727.303039611817.8040063981
165.699157916781.479995951281.377388333737.313708829562.654769904841.18353128726-0.111369667013-0.130451057598-0.303181603664-0.6660142009680.1707038940010.453093749668-0.540637594495-0.980718804672-0.08028568897820.9346356805250.133938204937-0.0877466100831.523538972790.1501141088090.792913300709-13.17579375113.708316248922.4871191646
170.165707377147-0.15124830294-0.2191034076098.509584857235.417856133443.547907718960.8517956542060.666945955706-0.88943955451-0.551775288248-2.61326143864-0.2026728829910.952528721646-1.300197186592.833717072741.473652885810.0379948387607-0.001740850684661.695224591440.2729159342411.31046027915-17.87795587512.911160125135.5516351761
182.694503835921.55355086692.546224415367.98894888615-4.229017814937.01638091904-0.9178120922690.0644717039761-1.002259799791.604676872711.411573466630.754900408705-0.798090125866-0.722462702860.516920424690.6216813050890.3467357087130.2027718061281.760945921890.02320548142111.28824393357-18.934861815314.926843723138.9560577251
195.536659989030.231033005803-0.5904016999574.79061819224.372056325376.11474546756-0.89826441587-1.61372872973-0.5989178259920.2100468820431.111868078890.4005597289290.3040297928150.117816257475-0.1241021528770.7443451893550.272645018870.08499271984831.093748275410.2206191026790.656851576417-10.057497608410.637335674333.2844980881
205.296814782951.25430468003-3.343172684532.379347478890.4749720016022.8807615581-2.471868503062.949009249570.948516155613-2.180152930911.117254230120.140639517387-1.23780066066-1.26268276222-0.4316903408831.995553329140.450368125634-0.3813449516081.95033791062-0.1975189045821.40191252-18.639125982631.850663218226.1235596012
215.700846823472.46202319971-1.614013606383.956888020390.9740553981472.32643553576-0.58316901688-1.99492827632-1.83452335881.838797886240.06649840247590.694470816597-0.826220960038-0.03067087130640.1463729681760.6719001622320.4388546089820.1683912390231.299905380430.1050076114110.721827132313-8.2642532821316.766785443129.8499024649
224.6247181327-0.6090003921850.9420820948645.26675312024-0.05958618452481.347596616341.24925596126-0.2099829586490.623354093480.672291463019-0.593591103739-0.798038732958-0.367084365887-1.964216767550.07622661121661.388428102690.340841015718-0.02949245797271.420815215380.3355216291181.042084882954.0281283972-0.97420543677941.705629317
231.71028914242-1.14546406229-0.4938995509722.4656665285-0.7241718040950.787828926912-0.401266010944-1.04203468517-0.280226321049-0.227734958377-0.1711641379630.654881719979-0.225831879299-0.261781534992-2.793586837690.5227208176210.819029960415-0.3306239864543.661371650550.7458609732761.08973470263-16.683647118412.554633381531.4173324395
243.58410693722.890635836491.017136309213.56286427232-0.4092173787123.474524801040.2832787855570.08743241229451.013346057460.123179992642-0.3748725092650.352169527947-0.4078392631390.3874122557810.09380182876870.8138745348450.195915844612-0.0235172836090.687366515403-0.02441977229580.9360323142383.1283872548827.826530199223.0579161537
252.61788983114-1.889903199220.8545586207912.094334340851.979738849869.2506566267-0.166354526267-3.870517082940.4312469158642.445591690350.3766955791660.912839363618-0.268984242955-0.508867570583-0.09060281264091.230618946530.05350504062890.171667864241.043641929870.008945979885310.9236534789925.8817153477426.562004342435.2507980696
261.236560217771.695209131371.196480975626.30117665419-1.960960125847.21364155439-0.331785494604-0.029043462024-0.190842020091.68276667737-0.8849426115151.30462547617-1.98355598582-1.136698988380.8602192788231.189861636490.192230986909-0.1147149128121.07885795332-0.1114486404070.98920138657414.214272984231.864093694131.4235798815
272.962714786860.970391892157-0.865811803733.409718472110.6982896874247.211829131940.10144439822-0.355675442218-0.260988455460.7224794794860.340274596698-0.502377709010.6563242936340.6831222730510.04531589711990.6545919370850.04930711347-0.1088506068841.009282477070.04086286183211.0280878352123.004546595818.163379538425.7419474254
283.796168282962.22917683540.7006855232336.83052427033-0.5378601146815.463522585030.00616394029583-0.515125036525-0.474285114350.4827496863880.35416022168-0.8982955906371.397543706970.4438543625990.1939020270950.7771080341190.290364551443-0.09688478366860.9728824889310.06064172833450.7660120673315.926552234615.815670919127.5275506717
293.77593809609-0.4368031837090.8098499653324.06777925406-1.069204875896.78363810391-0.882413993955-0.6522146135620.3747407450390.3970679809890.0786665462787-0.11017621899-0.739579048550.5416743572010.3165817054210.7140482853970.1440111284610.08515353140020.7325187002130.0007467935698970.71804676554112.117356541920.84038989530.1533445083
304.874763260651.764994464830.4536383790153.18576559001-2.034869102264.106232268260.185998606787-0.736657209098-0.5670647213450.4404276791440.6922544432730.7385290892470.0973575538264-0.321386080437-0.3629289979820.8052809037420.177112500190.0768909743920.889556811661-0.06405316381880.79035998025510.555219249815.518935641829.4056293269
318.692325650583.122910868480.5768974038121.209004762110.4254098254515.32235010991-0.7720940581090.213539656578-1.24566946524-1.17334824955-0.1278078873892.33641850935-0.6409598282311.331213017051.095658361041.281710773990.30674410004-0.05828287830760.8018888428180.02311207688731.2721494740718.22917408222.968874247326.278226266
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 57 )AA2 - 571 - 56
22chain 'A' and (resid 58 through 86 )AA58 - 8657 - 85
33chain 'A' and (resid 87 through 119 )AA87 - 11986 - 118
44chain 'A' and (resid 120 through 132 )AA120 - 132119 - 131
55chain 'A' and (resid 500 through 500 )AB500
66chain 'B' and (resid 2 through 33 )BC2 - 331 - 32
77chain 'B' and (resid 34 through 41 )BC34 - 4133 - 40
88chain 'B' and (resid 42 through 64 )BC42 - 6441 - 63
99chain 'B' and (resid 65 through 74 )BC65 - 7464 - 73
1010chain 'B' and (resid 75 through 86 )BC75 - 8674 - 85
1111chain 'B' and (resid 87 through 104 )BC87 - 10486 - 103
1212chain 'B' and (resid 105 through 119 )BC105 - 119104 - 118
1313chain 'B' and (resid 120 through 133 )BC120 - 133119 - 132
1414chain 'B' and (resid 500 through 500 )BD500
1515chain 'C' and (resid 1 through 12 )CE1 - 121 - 12
1616chain 'C' and (resid 13 through 56 )CE13 - 5613 - 56
1717chain 'C' and (resid 57 through 64 )CE57 - 6457 - 64
1818chain 'C' and (resid 65 through 74 )CE65 - 7465 - 74
1919chain 'C' and (resid 75 through 102 )CE75 - 10275 - 102
2020chain 'C' and (resid 103 through 110 )CE103 - 110103 - 110
2121chain 'C' and (resid 111 through 119 )CE111 - 119111 - 119
2222chain 'C' and (resid 120 through 133 )CE120 - 133120 - 133
2323chain 'C' and (resid 500 through 500 )CF500
2424chain 'D' and (resid 0 through 33 )DG0 - 331 - 34
2525chain 'D' and (resid 34 through 41 )DG34 - 4135 - 42
2626chain 'D' and (resid 42 through 56 )DG42 - 5643 - 57
2727chain 'D' and (resid 57 through 75 )DG57 - 7558 - 76
2828chain 'D' and (resid 76 through 86 )DG76 - 8677 - 87
2929chain 'D' and (resid 87 through 104 )DG87 - 10488 - 105
3030chain 'D' and (resid 105 through 132 )DG105 - 132106 - 133
3131chain 'D' and (resid 500 through 500 )DH500

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