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- PDB-2wc1: Three-dimensional Structure of the Nitrogen Fixation Flavodoxin (... -

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Basic information

Entry
Database: PDB / ID: 2wc1
TitleThree-dimensional Structure of the Nitrogen Fixation Flavodoxin (NifF) from Rhodobacter capsulatus at 2.2 A
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT / FLAVOPROTEIN
Function / homology
Function and homology information


nitrogen fixation / FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, long chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily ...Flavodoxin, long chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like / 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 speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsPerez-Dorado, I. / Bittel, C. / Hermoso, J.A. / Cortez, N. / Carrillo, N.
Citation
Journal: Int.J.Mol.Sci. / Year: 2013
Title: Structural and Phylogenetic Analysis of Rhodobacter Capsulatus Niff: Uncovering General Features of Nitrogen-Fixation (Nif)-Flavodoxins.
Authors: Perez-Dorado, I. / Bortolotti, A. / Cortez, N. / Hermoso, J.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization of a Flavodoxin Involved in Nitrogen Fixation in Rhodobacter Capsulatus.
Authors: Perez-Dorado, I. / Bortolotti, A. / Cortez, N. / Hermoso, J.A.
#2: Journal: Biochemistry / Year: 2005
Title: The Ferredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus: Molecular Structure and Catalytic Mechanism.
Authors: Nogues, I. / Perez-Dorado, I. / Frago, S. / Bittel, C. / Mayhew, S.G. / Gomez-Moreno, C. / Hermoso, J.A. / Medina, M. / Cortez, N. / Carrillo, N.
#3: Journal: FEBS Lett. / Year: 2003
Title: The Oxidant-Responsive Diaphorase of Rhodobacter Capsulatus is a Ferredoxin (Flavodoxin)-Nadp(H) Reductase.
Authors: Bittel, C. / Tabares, L.C. / Armesto, M. / Carrillo, N. / Cortez, N.
#4: Journal: Biochim.Biophys.Acta / Year: 1998
Title: Stopped-Flow Kinetic Studies of Low Potential Electron Carriers of the Photosynthetic Bacterium, Rhodobacter Capsulatus: Ferredoxin I and Niff.
Authors: Hallenbeck, P.C. / Gennaro, G.
#5: Journal: J.Bacteriol. / Year: 1996
Title: Cloning, Characterization, and Regulation of Niff from Rhodobacter Capsulatus.
Authors: Gennaro, G. / Hubner, P. / Sandmeier, U. / Yakunin, A.F. / Hallenbeck, P.C.
#6: Journal: J.Bacteriol. / Year: 1993
Title: Purification and Properties of a Nif-Specific Flavodoxin from the Photosynthetic Bacterium Rhodobacter Capsulatus.
Authors: Yakunin, A.F. / Gennaro, G. / Hallenbeck, P.C.
History
DepositionMar 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)20,2912
Polymers19,8341
Non-polymers4561
Water1,33374
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.400, 66.400, 121.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FLAVODOXIN


Mass: 19834.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Plasmid: PET32-FLD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P52967
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.4 Å3/Da / Density % sol: 63.7 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 25, 2004 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25.7 Å / Num. obs: 24830 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 22.4 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 26
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 22.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 8.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLV

1flv


Resolution: 2.17→25.66 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1425280.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1051 7 %RANDOM
Rwork0.246 ---
obs0.246 14974 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.1858 Å2 / ksol: 0.414581 e/Å3
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.41 Å20 Å20 Å2
2--5.41 Å20 Å2
3----10.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.17→25.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 31 74 1507
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.632.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.17→2.31 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 185 7.6 %
Rwork0.302 2253 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION5FMN.PARFMN.TOP

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