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- PDB-8a37: Crystal structure of PpSB1-LOV-K117E mutant (dark state), tetrago... -

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Basic information

Entry
Database: PDB / ID: 8a37
TitleCrystal structure of PpSB1-LOV-K117E mutant (dark state), tetragonal form
ComponentsSensory box protein
KeywordsSIGNALING PROTEIN / LOV domain / short LOV / PAS domain / Photocycle / Dimerization / Signaling blue light photoreceptor
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 / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsBatra-Safferling, R. / Granzin, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchFKZ 031A16 Germany
CitationJournal: To Be Published
Title: Crystal structure of PpSB1-LOV-K117E mutant (dark state), tetragonal form
Authors: Batra-Safferling, R. / Granzin, J. / Krauss, U.
History
DepositionJun 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 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)19,1803
Polymers18,6181
Non-polymers5622
Water1,56787
1
A: Sensory box protein
hetero molecules

A: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3606
Polymers37,2362
Non-polymers1,1254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5200 Å2
ΔGint-36 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.032, 65.032, 95.334
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

21A-654-

HOH

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Components

#1: Protein Sensory box protein


Mass: 18617.764 Da / Num. of mol.: 1 / Mutation: K117E
Source method: isolated from a genetically manipulated source
Details: K117E ENGINEERED MUTATION / Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria)
Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
Gene: PP_4629
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q88E39
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M di-Sodium phosphate, 20 % (w/v) PEG 4000

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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-F / Detector: PIXEL / Date: Nov 9, 2018
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.91→47.67 Å / Num. obs: 16542 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 39.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.019 / Rrim(I) all: 0.063 / Net I/σ(I): 21.1
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1087 / CC1/2: 0.873 / Rpim(I) all: 0.357 / % possible all: 100

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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: 5J3W

5j3w


Resolution: 1.91→41.42 Å / SU ML: 0.2138 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2236 791 4.81 %
Rwork0.1917 15661 -
obs0.1932 16452 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.48 Å2
Refinement stepCycle: LAST / Resolution: 1.91→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 38 87 1206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331138
X-RAY DIFFRACTIONf_angle_d0.60731535
X-RAY DIFFRACTIONf_chiral_restr0.0457162
X-RAY DIFFRACTIONf_plane_restr0.0038202
X-RAY DIFFRACTIONf_dihedral_angle_d13.7607451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-2.060.32931520.25143031X-RAY DIFFRACTION99.04
2.06-2.260.27651640.2123062X-RAY DIFFRACTION99.81
2.26-2.590.23311600.20553098X-RAY DIFFRACTION99.94
2.59-3.270.22141500.21093148X-RAY DIFFRACTION100
3.27-41.420.2071650.17293322X-RAY DIFFRACTION99.97
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)
16.035619671580.8180471102090.2162539281125.323976102491.044949078824.545905970930.05377765719470.0506074815568-0.135309221287-0.1237271282250.2501165615010.2271629945090.566895824272-0.11552290923-0.3701994477140.337246278638-0.0164623883141-0.04113514331230.3284187223420.02415540199040.307724121587-23.9468936852-18.29027355373.0253793575
24.233403954940.212685898605-1.696035773922.73611609409-1.139048893143.22093161465-0.02281074938010.4704865337550.0168970021266-0.02758641822640.105868724670.3121616540640.102944306295-0.715150182521-0.0278444566440.304499747701-0.03556826124310.006151134917520.4848910093550.01276117810650.347745527461-17.2864721252-13.7706995353-13.0115810916
33.770288777440.522954465001-1.53726435752.18128464610.05146083487623.5467481050.2087244881480.2994396146470.207064036078-0.115119066992-0.123334662907-0.0109166918608-0.1447976075-0.228716969714-0.09123023161490.2814877043270.009692957099320.03759597106480.3789591245010.02374327780680.320037255903-6.13071234689-12.5680906469-16.2554810535
40.639232422938-0.5656827749170.3383059030220.632309903406-0.874055320273.241761857380.757682521923-0.555650868176-0.733524795948-0.738705283957-0.241249563997-0.01328022958631.90248855166-0.777232475125-0.3149589935850.94278726773-0.179374951887-0.08632590741570.7844991790010.0640309597950.812698712172-15.477079595-32.8477827861-10.7071533964
52.64903572481-0.478670480741-1.001332982125.58808487393-0.8126335501673.27016190704-0.21238265297-0.02590751466030.02961125690740.01774593903660.5100118596430.1398206506430.1726766639560.0208293636725-0.3151392165530.332703750018-0.00690501146680.06689007707170.380112914508-0.01743759148160.369969583431-9.94441514089-14.9938051067-8.36757888098
64.803699938991.203812816970.7342268384381.517792485990.5640919574441.82619529580.562491693065-0.7855806191831.211622158890.834739049703-0.181263321993-0.509681334157-1.181235550010.743066557467-0.2409415212390.890385738585-0.1557533734990.05066070796920.560648229949-0.08871989904230.950324461244.204950609394.01233785036-4.74034835652
71.87074079242-1.38368819203-1.061103736031.94134662482.636892943614.552312164020.416240538660.1329502679380.122476135396-0.253716753364-0.126805467180.359473140058-0.532006969316-0.000375291871149-0.1705855024770.329657153276-0.0399786611660.03202347476760.536210256318-0.03525859891710.370842597103-7.90541195222-15.4660994622-17.4645466144
81.999876465115.115072632822.000417395219.788450252789.427293668951.99921283013-10.2787772632-5.143528172518.4735116553-6.46991194594-2.8828049638111.551198546-6.76895326763-3.1740043228513.2818166340.6612520785010.0896865155396-0.6814282857470.902786615849-0.02557697753490.481493871247-9.77478792475-2.90722728396-24.579443582
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 1 through 13 )A1 - 131 - 13
22chain 'A' and (resid 14 through 48 )A14 - 4814 - 48
33chain 'A' and (resid 49 through 101 )A49 - 10149 - 101
44chain 'A' and (resid 102 through 110 )A102 - 110102 - 110
55chain 'A' and (resid 111 through 119 )A111 - 119111 - 119
66chain 'A' and (resid 120 through 133 )A120 - 133120 - 133
77chain 'A' and (resid 500 through 500 )B500
88chain 'A' and (resid 501 through 501 )C501

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