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- PDB-5fnz: F206W mutant of FAD synthetase from Corynebacterium ammoniagenes -

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Basic information

Entry
Database: PDB / ID: 5fnz
TitleF206W mutant of FAD synthetase from Corynebacterium ammoniagenes
ComponentsRIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
KeywordsTRANSFERASE / RIBOFLAVIN KINASE / NUCLEOTIDE-BINDING / ATP- BINDING / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


riboflavin kinase / FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / ATP binding
Similarity search - Function
Riboflavin kinase, bacterial / FAD synthetase / FAD synthetase / Riboflavin kinase domain, bacterial/eukaryotic / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase-like / Riboflavin kinase domain superfamily / HUPs ...Riboflavin kinase, bacterial / FAD synthetase / FAD synthetase / Riboflavin kinase domain, bacterial/eukaryotic / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase-like / Riboflavin kinase domain superfamily / HUPs / Elongation Factor Tu (Ef-tu); domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE / Bifunctional riboflavin kinase/FMN adenylyltransferase
Similarity search - Component
Biological speciesCORYNEBACTERIUM AMMONIAGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsMartinez-Julvez, M. / Herguedas, B. / Milagros, M.
CitationJournal: Sci Rep / Year: 2017
Title: The trimer interface in the quaternary structure of the bifunctional prokaryotic FAD synthetase from Corynebacterium ammoniagenes.
Authors: Serrano, A. / Sebastian, M. / Arilla-Luna, S. / Baquedano, S. / Herguedas, B. / Velazquez-Campoy, A. / Martinez-Julvez, M. / Medina, M.
History
DepositionNov 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
B: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3916
Polymers73,8432
Non-polymers5484
Water1,856103
1
A: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
B: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
hetero molecules

A: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
B: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
hetero molecules

A: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
B: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,17318
Polymers221,5286
Non-polymers1,64412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
Buried area17440 Å2
ΔGint-210.5 kcal/mol
Surface area83020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.477, 133.477, 133.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 338 / Label seq-ID: 1 - 338

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF / FLAVOKINASE / FAD PYROPHOSPHORYLASE / FAD SYNTHASE


Mass: 36921.395 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM AMMONIAGENES (bacteria)
Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q59263, riboflavin kinase, FAD synthase, riboflavin kinase
#2: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATION F206W

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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: 2.72 Å3/Da / Density % sol: 54.86 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.5 M LI2SO4, 100 MM HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.52→47.19 Å / Num. obs: 26874 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.2
Reflection shellResolution: 2.52→2.65 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.1 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X0K

2x0k


Resolution: 2.52→40 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.886 / SU B: 10.044 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.576 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 200-204 AND 259-263 OF CHAIN A AND 201-202 AND 261-263 OF CHAIN B COULD NOT BE REFINED BECAUSE OF THE LACK OF ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.26281 1346 5 %RANDOM
Rwork0.20964 ---
obs0.21231 25497 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.708 Å2
Refinement stepCycle: LAST / Resolution: 2.52→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5099 0 28 103 5230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.025230
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9517124
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56123.843242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.04915812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6551536
X-RAY DIFFRACTIONr_chiral_restr0.0830.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213995
X-RAY DIFFRACTIONr_gen_planes_other
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 394 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.518→2.583 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 80 -
Rwork0.344 1556 -
obs--88.82 %

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