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- PDB-1yob: C69A Flavodoxin II from Azotobacter vinelandii -

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Basic information

Entry
Database: PDB / ID: 1yob
TitleC69A Flavodoxin II from Azotobacter vinelandii
ComponentsFlavodoxin 2
KeywordsELECTRON TRANSPORT / flavodoxin II / azotobacter vinelandii / alpha-beta fold / non-covalently bound FMN
Function / homology
Function and homology information


nitrogen fixation / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / 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 2
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAlagaratnam, S. / van Pouderoyen, G. / Pijning, T. / Dijkstra, B.W. / Cavazzini, D. / Rossi, G.L. / Canters, G.W.
CitationJournal: Protein Sci. / Year: 2005
Title: A crystallographic study of Cys69Ala flavodoxin II from Azotobacter vinelandii: structural determinants of redox potential
Authors: Alagaratnam, S. / van Pouderoyen, G. / Pijning, T. / Dijkstra, B.W. / Cavazzini, D. / Rossi, G.L. / Van Dongen, W.M. / van Mierlo, C.P. / van Berkel, W.J. / Canters, G.W.
History
DepositionJan 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavodoxin 2
B: Flavodoxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,52210
Polymers39,0332
Non-polymers1,4898
Water3,891216
1
A: Flavodoxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3576
Polymers19,5171
Non-polymers8415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flavodoxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1654
Polymers19,5171
Non-polymers6483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.013, 70.544, 132.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flavodoxin 2 / FLAVODOXIN II


Mass: 19516.609 Da / Num. of mol.: 2 / Mutation: C69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Plasmid: pC69Afld / Production host: Escherichia coli (E. coli) / Strain (production host): TG2 / References: UniProt: P00324
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.44 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ammonium sulphate, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 11, 2003
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 18100 / Num. obs: 16669 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.66 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 16.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1766 / Rsym value: 0.492 / % possible all: 85.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
EPMRphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RCF based model made by the 3D-PSSM server

1rcf


Resolution: 2.25→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 872 5 %random
Rwork0.222 ---
all-18100 --
obs-16669 92.1 %-
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å20 Å20 Å2
2--2.1 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 92 216 3068
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.35
X-RAY DIFFRACTIONc_mcangle_it2.14
X-RAY DIFFRACTIONc_scbond_it2.18
X-RAY DIFFRACTIONc_scangle_it3.14

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