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- PDB-7eg5: FMN-bound form of YviC from Lactococcus lactis subsp. lactis Il1403 -

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Basic information

Entry
Database: PDB / ID: 7eg5
TitleFMN-bound form of YviC from Lactococcus lactis subsp. lactis Il1403
ComponentsFMN-binding protein
KeywordsFLAVOPROTEIN / fmn binding
Function / homologyPyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / FMN-binding split barrel / FLAVIN MONONUCLEOTIDE / FMN-binding protein
Function and homology information
Biological speciesLactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSugiura, N. / Nakanishi, T. / Kitamura, M.
CitationJournal: To Be Published
Title: FMN-bound form of YviC from Lactococcus lactis subsp. lactis Il1403
Authors: Sugiura, N. / Nakanishi, T. / Kitamura, M.
History
DepositionMar 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: FMN-binding protein
B: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2074
Polymers28,2952
Non-polymers9132
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-29 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.509, 94.801, 142.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein FMN-binding protein


Mass: 14147.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
Strain: IL1403 / Gene: yviC, L164222 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9CDV0
#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.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES (pH 7.62), 1.7 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→19.93 Å / Num. obs: 20447 / % possible obs: 99.3 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.1
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.378 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLM

1flm


Resolution: 1.96→19.93 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.762 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1037 5.1 %RANDOM
Rwork0.199 ---
obs0.2 19375 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.96→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 62 16 2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132092
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171984
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.6462832
X-RAY DIFFRACTIONr_angle_other_deg1.3441.5744616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3985248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89323.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91915384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.708158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 81 -
Rwork0.207 1375 -
obs--98.31 %

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