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- PDB-8q5e: Crystal structure of PpSB1-LOV protein from Pseudomonas putida wi... -

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Basic information

Entry
Database: PDB / ID: 8q5e
TitleCrystal structure of PpSB1-LOV protein from Pseudomonas putida with covalent FMN
ComponentsSensory box protein
KeywordsSIGNALING PROTEIN / covalent flavinylation
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 / NICKEL (II) ION / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Fixing Flavins: Hijacking a Flavin Transferase for Equipping Flavoproteins with a Covalent Flavin Cofactor.
Authors: Tong, Y. / Kaya, S.G. / Russo, S. / Rozeboom, H.J. / Wijma, H.J. / Fraaije, M.W.
History
DepositionAug 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensory box protein
B: Sensory box protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3265
Polymers32,3542
Non-polymers9713
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-35 kcal/mol
Surface area14150 Å2
Unit cell
Length a, b, c (Å)153.926, 153.926, 36.039
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 135 / Label seq-ID: 1 - 135

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Sensory box protein


Mass: 16177.114 Da / Num. of mol.: 2 / Mutation: D60D R61A D62A Q63S L64G G65A R66T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: PP_4629 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q88E39
#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
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% PEG3350, 10 mM MgCl 2 , 5 mM NiCl 2 and 100 mM HEPES buffer pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.4→44.43 Å / Num. obs: 11764 / % possible obs: 94.7 % / Redundancy: 1.9 % / CC1/2: 0.968 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.052 / Rrim(I) all: 0.078 / Χ2: 0.95 / Net I/σ(I): 11.8 / Num. measured all: 22897
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 97 % / Redundancy: 2 % / Rmerge(I) obs: 0.458 / Num. measured all: 2476 / Num. unique obs: 1262 / CC1/2: 0.722 / Rpim(I) all: 0.39 / Rrim(I) all: 0.604 / Χ2: 0.66 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0403refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.511 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.435 / SU ML: 0.267 / Cross valid method: FREE R-VALUE / ESU R: 0.567 / ESU R Free: 0.328
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2944 602 5.155 %
Rwork0.227 11077 -
all0.23 --
obs-11679 93.973 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 73.384 Å2
Baniso -1Baniso -2Baniso -3
1--0.151 Å2-0.075 Å20 Å2
2---0.151 Å20 Å2
3---0.489 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 61 0 2217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122250
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162106
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.6433034
X-RAY DIFFRACTIONr_angle_other_deg0.5641.5724812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4755268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.017526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78410392
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.94410120
X-RAY DIFFRACTIONr_chiral_restr0.0760.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_nbd_refined0.230.2469
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21976
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21128
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21340
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4070.225
X-RAY DIFFRACTIONr_nbd_other0.3750.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.60.24
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.4020.22
X-RAY DIFFRACTIONr_mcbond_it8.6967.011078
X-RAY DIFFRACTIONr_mcbond_other8.6967.011078
X-RAY DIFFRACTIONr_mcangle_it11.83812.5631344
X-RAY DIFFRACTIONr_mcangle_other11.83412.5621345
X-RAY DIFFRACTIONr_scbond_it9.7787.6271172
X-RAY DIFFRACTIONr_scbond_other9.7557.6241170
X-RAY DIFFRACTIONr_scangle_it13.64413.6391690
X-RAY DIFFRACTIONr_scangle_other13.6413.6391691
X-RAY DIFFRACTIONr_lrange_it17.14784.9319395
X-RAY DIFFRACTIONr_lrange_other17.14784.9289396
X-RAY DIFFRACTIONr_ncsr_local_group_10.1660.053937
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.165620.05007
12AX-RAY DIFFRACTIONLocal ncs0.165620.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.432360.2938160.2988800.8840.95196.81820.284
2.462-2.5290.384490.2838220.2899040.9380.95696.34960.262
2.529-2.6020.382500.2567900.2638760.9240.96595.89040.225
2.602-2.6820.302620.2547450.2588360.9510.96396.53110.228
2.682-2.7690.361360.2527740.2578460.910.96695.74470.223
2.769-2.8660.247410.2586760.2577500.960.96495.60.223
2.866-2.9740.363300.2487530.2528070.9210.96397.0260.218
2.974-3.0940.311480.2276200.2337100.9310.9794.08450.211
3.094-3.2310.23300.2346250.2347100.9650.96892.25350.217
3.231-3.3880.35330.2395820.2466720.9320.96891.51790.234
3.388-3.5690.343260.2755820.2786600.9340.95992.12120.267
3.569-3.7840.489210.4054840.4085860.8310.91486.17750.376
3.784-4.0420.297320.2655160.2675940.960.9692.25590.282
4.042-4.3620.232240.1844750.1875240.9690.98195.2290.217
4.362-4.7720.172190.1364210.1374730.9810.98993.02330.162
4.772-5.3250.297160.1614190.1664630.9590.98693.95250.201
5.325-6.130.229140.1863420.1883930.9750.9890.58520.221
6.13-7.460.37380.1852890.1893280.960.98190.54880.242
7.46-10.3580.222180.1462170.1512570.9720.98991.43970.201
10.358-38.5110.23290.2151290.2161570.9680.96887.89810.28

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