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- PDB-4uzf: R66E mutant of FAD synthetase from Corynebacterium ammoniagenes -

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Basic information

Entry
Database: PDB / ID: 4uzf
TitleR66E 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: Biochim.Biophys.Acta / Year: 2015
Title: Quaternary Organization in a Bifunctional Prokaryotic Fad Synthetase: Involvement of an Arginine at its Adenylyltransferase Module on the Riboflavin Kinase Activity.
Authors: Serrano, A. / Sebastian, M. / Arilla-Luna, S. / Baquedano, S. / Pallares, M.C. / Lostao, A. / Herguedas, B. / Velazquez-Campoy, A. / Martinez-Julvez, M. / Medina, M.
History
DepositionSep 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: 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

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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)74,2576
Polymers73,7092
Non-polymers5484
Water3,099172
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)222,77018
Polymers221,1266
Non-polymers1,64412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area19030 Å2
ΔGint-188.6 kcal/mol
Surface area82310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.834, 133.834, 133.834
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


Mass: 36854.281 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM AMMONIAGENES (bacteria)
Plasmid: PET28 / 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.: 172 / 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: 2.76 Å3/Da / Density % sol: 55.41 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.5 M LI2SO4 AND 0.1 M HEPES-NAOH 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→44.61 Å / Num. obs: 26991 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.4
Reflection shellResolution: 2.52→2.65 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.7 / % possible all: 89.8

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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: 2.52→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.826 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.579 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 258-263 IN CHAIN A AND 260-262 IN CHAIN B WERE NOT REFINED DUE TO THE LACK OF LOCAL ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.25167 1356 5 %RANDOM
Rwork0.20034 ---
obs0.20294 25602 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.28 Å2
Refinement stepCycle: LAST / Resolution: 2.52→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5143 0 28 172 5343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.025273
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9557180
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40824.098244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50115825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5751534
X-RAY DIFFRACTIONr_chiral_restr0.0790.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214032
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: 2.516→2.581 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 79 -
Rwork0.339 1512 -
obs--80.56 %

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