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- PDB-6ohk: Crystal structure of Fusobacterium nucleatum flavodoxin mutant K1... -

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Basic information

Entry
Database: PDB / ID: 6ohk
TitleCrystal structure of Fusobacterium nucleatum flavodoxin mutant K13G bound to flavin mononucleotide
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / flavodoxin / reduction potential / flavin mononucleotide / electron transfer
Function / homology
Function and homology information


FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, long chain / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKolesnikov, M. / Murphy, M.E.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Protein Sci. / Year: 2019
Title: Structural insight into the high reduction potentials observed for Fusobacterium nucleatum flavodoxin.
Authors: Mothersole, R.G. / Macdonald, M. / Kolesnikov, M. / Murphy, M.E.P. / Wolthers, K.R.
History
DepositionApr 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6093
Polymers19,0611
Non-polymers5482
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.090, 67.250, 72.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flavodoxin


Mass: 19060.713 Da / Num. of mol.: 1 / Mutation: K13G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RFH4
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 21% PEG 3350, 0.23M magnesium chloride, 0.1M HEPES pH 7.5
Temp details: Cold Room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97965 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 1.2→36.44 Å / Num. obs: 55823 / % possible obs: 99.2 % / Redundancy: 6.594 % / Biso Wilson estimate: 12.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Χ2: 1.073 / Net I/σ(I): 17.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.233.8310.5322.5337550.8430.61692
1.23-1.265.0030.483.4839150.9050.53797.5
1.26-1.36.3290.4344.5738990.9310.474100
1.3-1.347.1660.3725.937760.960.401100
1.34-1.397.0230.3136.936860.9680.338100
1.39-1.436.9780.2568.3735390.9790.276100
1.43-1.497.0330.20710.3934440.9880.224100
1.49-1.557.2870.16113.233100.9930.173100
1.55-1.627.040.12316.0231760.9940.132100
1.62-1.77.1560.10618.5630570.9950.114100
1.7-1.797.0770.08621.5429000.9960.093100
1.79-1.97.2910.06926.0727670.9970.074100
1.9-2.036.8450.05729.3625860.9970.062100
2.03-2.197.0820.05133.1124280.9980.055100
2.19-2.46.8630.04734.7222530.9980.0599.9
2.4-2.686.8390.04536.3320180.9980.04999.9
2.68-3.16.5890.04237.3818140.9980.04599.9
3.1-3.796.5050.03939.3515440.9990.04299.6
3.79-5.376.4370.03739.6312300.9980.0499.8
5.37-36.446.1720.03738.397260.9970.04199.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→36.44 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.3
RfactorNum. reflection% reflection
Rfree0.164 2792 5 %
Rwork0.1514 --
obs0.1521 55815 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.91 Å2 / Biso mean: 17.3804 Å2 / Biso min: 7.01 Å2
Refinement stepCycle: final / Resolution: 1.2→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 64 235 1645
Biso mean--18.09 27.73 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131424
X-RAY DIFFRACTIONf_angle_d1.2031921
X-RAY DIFFRACTIONf_chiral_restr0.094209
X-RAY DIFFRACTIONf_plane_restr0.009237
X-RAY DIFFRACTIONf_dihedral_angle_d19.745506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1999-1.22060.27151240.25862340246491
1.2206-1.24280.25411330.24062535266895
1.2428-1.26670.22641370.20532601273899
1.2667-1.29250.19261400.186326492789100
1.2925-1.32060.20591380.182626222760100
1.3206-1.35140.19851380.172726342772100
1.3514-1.38520.18021400.167726552795100
1.3852-1.42260.18551380.166126282766100
1.4226-1.46450.19431400.160226552795100
1.4645-1.51180.17711400.159126572797100
1.5118-1.56580.18631410.149526702811100
1.5658-1.62850.15671390.138726572796100
1.6285-1.70260.16571410.142326662807100
1.7026-1.79240.16261390.137226512790100
1.7924-1.90460.1381420.13626922834100
1.9046-2.05170.15631400.132126692809100
2.0517-2.25810.14881430.134327182861100
2.2581-2.58480.14411430.138627032846100
2.5848-3.25630.16841440.153527442888100
3.2563-36.45680.15091520.152828773029100

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