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- PDB-6ohl: Crystal structure of Fusobacterium nucleatum flavodoxin bound to ... -

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Basic information

Entry
Database: PDB / ID: 6ohl
TitleCrystal structure of Fusobacterium nucleatum flavodoxin 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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)19,8735
Polymers19,1331
Non-polymers7414
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.872, 118.872, 103.375
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

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Components

#1: Protein Flavodoxin


Mass: 19132.840 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.73 Å3/Da / Density % sol: 67.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 42-46% PEG 600, 0.16-0.18 M calcium acetate, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 23672 / % possible obs: 98.3 % / Redundancy: 9.9 % / Biso Wilson estimate: 19.92 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.03 / Rrim(I) all: 0.097 / Χ2: 0.831 / Net I/σ(I): 6.3 / Num. measured all: 235021
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.883.80.4929120.7890.2510.5560.70576.6
1.88-1.924.60.46110960.8370.220.5140.72592.1
1.92-1.955.90.41611660.9010.1790.4550.73798.1
1.95-1.998.10.38711910.9390.1430.4140.72199.9
1.99-2.0410.30.3811840.9650.1240.40.737100
2.04-2.0810.60.30312050.9760.0980.3190.759100
2.08-2.1410.80.28311940.9820.090.2970.781100
2.14-2.1910.80.25412020.9850.0810.2660.803100
2.19-2.2610.90.2311970.9890.0730.2410.829100
2.26-2.3310.90.20611850.990.0660.2170.815100
2.33-2.4110.90.18211950.9920.0580.1910.84100
2.41-2.51110.17311940.9930.0550.1810.862100
2.51-2.63110.14312140.9950.0450.150.855100
2.63-2.76110.13712000.9950.0430.1440.857100
2.76-2.94110.10711960.9960.0340.1120.9100
2.94-3.1611.10.08212090.9980.0260.0850.892100
3.16-3.4811.10.0612220.9990.0190.0630.924100
3.48-3.9911.10.04812090.9990.0150.0510.935100
3.99-5.02110.039123410.0120.0410.865100
5.02-5010.60.03712670.9990.0120.0380.81399.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.34 Å25.07 Å
Translation4.34 Å25.07 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
HKL-2000data scaling
PHASER2.7.16phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→25.066 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1912 2000 8.45 %
Rwork0.1675 21667 -
obs0.1695 23667 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.46 Å2 / Biso mean: 22.8975 Å2 / Biso min: 10.17 Å2
Refinement stepCycle: final / Resolution: 1.85→25.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 56 145 1531
Biso mean--29.44 29.99 -
Num. residues----167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121425
X-RAY DIFFRACTIONf_angle_d1.0241925
X-RAY DIFFRACTIONf_chiral_restr0.067209
X-RAY DIFFRACTIONf_plane_restr0.006236
X-RAY DIFFRACTIONf_dihedral_angle_d4.7891129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89620.27311160.22641252136881
1.8962-1.94750.25621390.20581505164496
1.9475-2.00480.23771420.195615371679100
2.0048-2.06940.23941450.172515801725100
2.0694-2.14340.21481420.169215471689100
2.1434-2.22910.21531450.177715661711100
2.2291-2.33050.21151440.175115661710100
2.3305-2.45330.19041450.171715621707100
2.4533-2.60680.19831440.172615601704100
2.6068-2.80790.20371460.186115801726100
2.8079-3.090.21071460.183915811727100
3.09-3.5360.18261450.167715761721100
3.536-4.4510.13951480.13815991747100
4.451-25.06830.1641530.144616561809100

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