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- PDB-4j2p: Crystal structure of LuxF from Photobacterium leiognathi -

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Basic information

Entry
Database: PDB / ID: 4j2p
TitleCrystal structure of LuxF from Photobacterium leiognathi
ComponentsNon-fluorescent flavoprotein
KeywordsLUMINESCENT PROTEIN / incomplete beta-barrel / modified 7-stranded barrel / myr-FMN binding / myr-FMN
Function / homology
Function and homology information


alkanal monooxygenase (FMN-linked) activity
Similarity search - Function
Bacterial luciferase, conserved site / Bacterial luciferase subunits signature. / Bacterial luciferase/NFP / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Non-fluorescent flavoprotein
Similarity search - Component
Biological speciesPhotobacterium leiognathi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsWinkler, A. / Macheroux, P. / Gruber, K.
CitationJournal: Biochim. Biophys. Acta / Year: 2015
Title: Structural and biochemical properties of LuxF from Photobacterium leiognathi.
Authors: Bergner, T. / Tabib, C.R. / Winkler, A. / Stipsits, S. / Kayer, H. / Lee, J. / Malthouse, J.P. / Mayhew, S. / Muller, F. / Gruber, K. / Macheroux, P.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-fluorescent flavoprotein


Theoretical massNumber of molelcules
Total (without water)27,3411
Polymers27,3411
Non-polymers00
Water3,117173
1
A: Non-fluorescent flavoprotein

A: Non-fluorescent flavoprotein


Theoretical massNumber of molelcules
Total (without water)54,6822
Polymers54,6822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455y-1/2,x+1/2,-z+1/21
Buried area3190 Å2
ΔGint-27 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.180, 93.180, 115.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-356-

HOH

21A-401-

HOH

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Components

#1: Protein Non-fluorescent flavoprotein / NFP / FP390


Mass: 27340.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium leiognathi (bacteria) / Gene: luxF / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P09142
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 293 K / Method: drop under oil / pH: 7
Details: 0.15M malic acid, 20% w/v polyethylene glycol 3,350, pH 7.0, drops under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2008
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.85→39.2 Å / Num. all: 22033 / Num. obs: 22033 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 35.345 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 41
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.85-1.950.663.14265773164199.7
1.95-2.10.3398.114901536791100
2.1-2.50.13920.858955560731100
2.5-30.05745.54553413755199.9
3-40.02691.584404030291100
4-60.019123.562258416011100
6-100.016121.1374645571100
10-200.012139.4617581501100
20-300.014109.2118120195.2
30-39.20.01256.785155.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.85 Å39.2 Å
Translation1.85 Å39.2 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NFP

1nfp


Resolution: 1.85→39.2 Å / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.17 / Isotropic thermal model: isotropic / σ(F): 0 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1103 5.01 %random
Rwork0.1706 ---
all0.1723 22033 --
obs0.1723 22031 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.63 Å2 / Biso mean: 41.0149 Å2 / Biso min: 17.75 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 0 173 1993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071868
X-RAY DIFFRACTIONf_angle_d1.0072528
X-RAY DIFFRACTIONf_chiral_restr0.071280
X-RAY DIFFRACTIONf_plane_restr0.004327
X-RAY DIFFRACTIONf_dihedral_angle_d13.826685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.93430.28111180.23725722690
1.9343-2.03630.291260.221826002726
2.0363-2.16380.29041210.204625872708
2.1638-2.33090.24181380.186925792717
2.3309-2.56540.22591480.184925842732
2.5654-2.93650.23081550.185625992754
2.9365-3.69930.1741350.159726462781
3.6993-39.20.16671620.142227612923
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)
14.42630.4486-0.68154.3147-0.48512.40390.10720.1387-0.3886-0.0752-0.0876-0.20070.18940.1042-0.04980.2460.0492-0.0070.1596-0.03110.2127-31.12714.091441.8998
20.13290.19970.06060.791-1.32784.0922-0.04630.1618-0.13860.25560.22860.1953-0.93540.7643-0.04240.70210.18720.05430.6650.10190.5226-24.171629.36528.3758
32.9403-0.26430.03271.2688-0.75130.52770.66891.1930.9539-0.4534-0.17670.0411-0.3144-0.28090.00450.41250.22590.09850.54330.17440.3475-40.786728.778328.6033
43.5360.45810.79891.6879-0.3863.169-0.0178-0.34250.18720.2025-0.0356-0.0888-0.21-0.22460.04020.17590.0148-0.010.1731-0.04250.1515-35.539323.730348.6638
58.53752.89060.90857.4117-1.12477.16840.2074-0.2661-0.57160.10470.06381.14850.6468-1.0574-0.21590.2872-0.0778-0.02210.28910.00480.5514-51.83089.80743.7654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:49)A1 - 49
2X-RAY DIFFRACTION2(chain A and resid 50:62)A50 - 62
3X-RAY DIFFRACTION3(chain A and resid 63:130)A63 - 130
4X-RAY DIFFRACTION4(chain A and resid 131:213)A131 - 213
5X-RAY DIFFRACTION5(chain A and resid 214:228)A214 - 228

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