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- PDB-1fue: FLAVODOXIN FROM HELICOBACTER PYLORI -

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Basic information

Entry
Database: PDB / ID: 1fue
TitleFLAVODOXIN FROM HELICOBACTER PYLORI
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT / flavoprotein / Helicobacter pylori / fmn
Function / homology
Function and homology information


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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsFreigang, J. / Diederichs, K. / Schaefer, K.P. / Welte, W. / Paul, R.
CitationJournal: Protein Sci. / Year: 2002
Title: Crystal structure of oxidized flavodoxin, an essential protein in Helicobacter pylori.
Authors: Freigang, J. / Diederichs, K. / Schafer, K.P. / Welte, W. / Paul, R.
History
DepositionSep 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)17,7612
Polymers17,3051
Non-polymers4561
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.130, 47.220, 48.310
Angle α, β, γ (deg.)90.00, 97.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FLAVODOXIN /


Mass: 17305.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZK53
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 1500, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
230 %(w/w)PEG15001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 27, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 5537 / Num. obs: 5346 / % possible obs: 96.6 % / Observed criterion σ(F): -10 / Observed criterion σ(I): -10 / Redundancy: 2.46 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.48 % / Rmerge(I) obs: 0.325 / Num. unique all: 530 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 13654
Reflection shell
*PLUS
% possible obs: 99.2 % / Mean I/σ(I) obs: 2.7

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.4→18.76 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 271006.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 536 10.4 %RANDOM
Rwork0.198 ---
all0.198 5144 --
obs0.198 5144 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.65 Å2 / ksol: 0.287 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1--14.86 Å20 Å23.97 Å2
2--4.22 Å20 Å2
3---10.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→18.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 31 32 1285
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it3.081.5
X-RAY DIFFRACTIONc_mcangle_it4.722
X-RAY DIFFRACTIONc_scbond_it4.582
X-RAY DIFFRACTIONc_scangle_it6.572.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 85 10.3 %
Rwork0.296 738 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3FMN.PARAMFMN.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.4 % / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66
X-RAY DIFFRACTIONc_mcbond_it3.081.5
X-RAY DIFFRACTIONc_scbond_it4.582
X-RAY DIFFRACTIONc_mcangle_it4.722
X-RAY DIFFRACTIONc_scangle_it6.572.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.31 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.296

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