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- PDB-3fni: Crystal structure of a diflavin flavoprotein A3 (all3895) from No... -

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Basic information

Entry
Database: PDB / ID: 3fni
TitleCrystal structure of a diflavin flavoprotein A3 (all3895) from Nostoc sp., Northeast Structural Genomics Consortium Target NsR431A
ComponentsPutative diflavin flavoprotein A 3
KeywordsOXIDOREDUCTASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Electron transport / Iron / Metal-binding / Transport
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / Oxidoreductases / FMN binding / metal ion binding
Similarity search - Function
: / ODP domain / ODP family beta lactamase / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / FMN-binding split barrel / Flavodoxin domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase ...: / ODP domain / ODP family beta lactamase / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / FMN-binding split barrel / Flavodoxin domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative diflavin flavoprotein A 3
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of a diflavin flavoprotein A3 (all3895) from Nostoc sp., Northeast Structural Genomics Consortium Target NsR431A
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Apr 9, 2014Group: Data collection
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative diflavin flavoprotein A 3


Theoretical massNumber of molelcules
Total (without water)17,0541
Polymers17,0541
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.096, 66.301, 75.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer

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Components

#1: Protein Putative diflavin flavoprotein A 3


Mass: 17053.957 Da / Num. of mol.: 1 / Fragment: residues 259-409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: all3895, dfa3 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8YQD8, Oxidoreductases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 7.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution:100 mM HEPES (pH 7.5), 40% PEG 4k, and 100 mM Magnesium Acetate. , Microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.96863 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 3, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 12344 / Num. obs: 12184 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.075 / Net I/σ(I): 25.44
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 12.4 / Num. unique all: 1235 / Rsym value: 0.157 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXthen SOLVE/RESOLVEmodel building
CNS1.2 & XtalViewrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 640762.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 586 5.1 %RANDOM
Rwork0.21 ---
all0.212 12038 --
obs0.21 11425 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.4613 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1--8.63 Å20 Å20 Å2
2--19.53 Å20 Å2
3----10.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 141 1289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.266 38 3.4 %
Rwork0.222 1081 -
obs-1081 92.2 %

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