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- PDB-29lw: Crystal structure of PpSB1-LOV protein from Pseudomonas putida in... -

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Basic information

Entry
Database: PDB / ID: 29lw
TitleCrystal structure of PpSB1-LOV protein from Pseudomonas putida in complex with 5-deazaflavin mononucleotide (5dFMN)
ComponentsSensory box protein
KeywordsFLAVOPROTEIN / 5-deaza FMN / complex / 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
Chem-9O9 / Sensory box protein
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Synth Biol / Year: 2026
Title: Engineered Escherichia coli Strains for Flavoprotein Research: From Production of Apoproteins to Incorporation of Flavin Derivatives.
Authors: Fan, X. / Widodo, W.S. / Rozeboom, H.J. / Fraaije, M.W.
History
DepositionMar 20, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.name
Revision 1.2Jul 1, 2026Group: 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

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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)34,35610
Polymers32,8932
Non-polymers1,4638
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-39 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.239, 61.875, 107.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sensory box protein


Mass: 16446.463 Da / Num. of mol.: 2
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-9O9 / 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol


Mass: 455.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N3O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M Ammonium formate, 0.1 M bistris propane pH 8.5
PH range: 6-8.5

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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: Jul 18, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.54→107.7 Å / Num. obs: 50710 / % possible obs: 98.8 % / Redundancy: 11.7 % / CC1/2: 1 / Net I/σ(I): 19.2
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 10 % / Num. unique obs: 19681 / CC1/2: 0.366 / % possible all: 78.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→53.58 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.576 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19023 2541 5 %RANDOM
Rwork0.1674 ---
obs0.16858 48098 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.568 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-0 Å2
2---0.63 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.54→53.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 98 284 2554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122334
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162193
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.8293145
X-RAY DIFFRACTIONr_angle_other_deg0.631.7965016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.858529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29510411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7941.7161090
X-RAY DIFFRACTIONr_mcbond_other1.7931.7171090
X-RAY DIFFRACTIONr_mcangle_it2.6443.071366
X-RAY DIFFRACTIONr_mcangle_other2.6453.0741367
X-RAY DIFFRACTIONr_scbond_it3.2712.1651244
X-RAY DIFFRACTIONr_scbond_other3.2742.1681245
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9383.7651780
X-RAY DIFFRACTIONr_long_range_B_refined7.13920.192768
X-RAY DIFFRACTIONr_long_range_B_other6.95317.912699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 157 -
Rwork0.326 3054 -
obs--85.58 %
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)
10.8902-0.1312-0.3761.23320.12451.26550.013-0.1214-0.06050.1054-0.04230.02370.06030.01140.02940.1633-0.00710.01460.05670.01310.0064-6.093111.4471-8.4114
20.974-0.4538-0.46631.52090.42890.76650.02720.00510.0234-0.20450.035-0.1182-0.0896-0-0.06220.1935-0.01160.03330.015-0.00050.01332.328113.1128-26.7495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 201
2X-RAY DIFFRACTION2B1 - 201

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