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- PDB-3vy2: N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (M... -

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Basic information

Entry
Database: PDB / ID: 3vy2
TitleN33D mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
ComponentsFMN-binding protein
KeywordsELECTRON TRANSPORT
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTakagi, R. / Nakanishi, T. / Kitamura, M.
CitationJournal: To be Published
Title: Crystal structure of N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
Authors: Takagi, R. / Nakanishi, T. / Kitamura, M.
History
DepositionSep 21, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2214
Polymers26,3082
Non-polymers9132
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-20 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.868, 83.038, 40.239
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FMN-binding protein


Mass: 13154.052 Da / Num. of mol.: 2 / Mutation: N33D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Miyazaki F / Gene: DvMF_2023 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46604
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 19.8% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 19, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 31712 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.196 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLM

1flm


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.285 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19202 1602 5.1 %RANDOM
Rwork0.17034 ---
obs0.17146 30085 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.06 Å2
2--0.69 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 62 235 2149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221952
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9922656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32222.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.75615308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.161518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211478
X-RAY DIFFRACTIONr_mcbond_it0.5671.51202
X-RAY DIFFRACTIONr_mcangle_it1.08121926
X-RAY DIFFRACTIONr_scbond_it1.6843750
X-RAY DIFFRACTIONr_scangle_it2.8054.5730
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 112 -
Rwork0.217 2200 -
obs--99.91 %

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