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- PDB-1wlk: L122E mutant of FMN-binding protein from Desulfovibrio vulgaris (... -

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Basic information

Entry
Database: PDB / ID: 1wlk
TitleL122E mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
ComponentsFMN-binding protein
KeywordsELECTRON TRANSPORT / Flavoprotein / FMN
Function / homology
Function and homology information


Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN-binding protein
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShibata, N. / Higuchi, Y.
CitationJournal: J.Biochem. / Year: 2007
Title: Determination of the role of the Carboxyl-terminal leucine-122 in FMN-binding protein by mutational and structural analysis.
Authors: Kitamura, M. / Terakawa, K. / Inoue, H. / Hayashida, T. / Suto, K. / Morimoto, Y. / Yasuoka, N. / Shibata, N. / Higuchi, Y.
History
DepositionJun 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMN-binding protein
B: FMN-binding protein
C: FMN-binding protein
D: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5018
Polymers52,6764
Non-polymers1,8254
Water7,566420
1
A: FMN-binding protein
B: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2514
Polymers26,3382
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-18 kcal/mol
Surface area10730 Å2
MethodPISA
2
C: FMN-binding protein
D: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2514
Polymers26,3382
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-20 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.164, 57.959, 62.018
Angle α, β, γ (deg.)90.00, 91.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FMN-binding protein


Mass: 13169.022 Da / Num. of mol.: 4 / Mutation: L122E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
Species: Desulfovibrio vulgaris / Strain: Miyazaki F / Production host: Escherichia coli (E. coli) / References: UniProt: Q46604
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG6000, sodium acetate, Tris , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→500 Å / Num. all: 33783 / Num. obs: 33783 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 7.3 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 102083.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1637 5 %RANDOM
Rwork0.184 ---
obs0.184 32810 97 %-
all-32810 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4564 Å2 / ksol: 0.342761 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.07 Å20 Å21.88 Å2
2--1.92 Å20 Å2
3---1.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 124 420 4252
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.256 172 5.5 %
Rwork0.207 2939 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4FMN.PARAM

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