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- PDB-5fo1: E301A mutant of FAD synthetase from Corynebacterium ammoniagenes -

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Basic information

Entry
Database: PDB / ID: 5fo1
TitleE301A 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: 2.45 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 1.2Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 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_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_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)74,1976
Polymers73,6492
Non-polymers5484
Water3,027168
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)222,59018
Polymers220,9466
Non-polymers1,64412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
Buried area18780 Å2
ΔGint-175.4 kcal/mol
Surface area84750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.965, 134.965, 134.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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


Mass: 36824.324 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM AMMONIAGENES (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q59263, riboflavin kinase, FAD synthase
#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.: 168 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATION E301A

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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: 2.74 Å3/Da / Density % sol: 55.13 % / 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: 2.45→47.72 Å / Num. obs: 30328 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 94.7

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Processing

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

2x0k


Resolution: 2.45→40 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.268 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 200 AND 260-262 OF CHAIN B COULD NOT BE REFINED BECAUSE OF THE LACK OF ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.25608 1533 5.1 %RANDOM
Rwork0.20873 ---
obs0.21107 28745 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.362 Å2
Refinement stepCycle: LAST / Resolution: 2.45→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5169 0 28 168 5365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195301
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9547219
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3615670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73223.893244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19515826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3421536
X-RAY DIFFRACTIONr_chiral_restr0.0780.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214057
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
LS refinement shellResolution: 2.446→2.509 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.491 106 -
Rwork0.382 1797 -
obs--89.38 %

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