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- PDB-2wsi: Crystal structure of yeast FAD synthetase (Fad1) in complex with FAD -

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Basic information

Entry
Database: PDB / ID: 2wsi
TitleCrystal structure of yeast FAD synthetase (Fad1) in complex with FAD
ComponentsFAD SYNTHETASE
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


Vitamin B2 (riboflavin) metabolism / FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide synthase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsLeulliot, N. / van Tilbeurgh, H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure of Yeast Fad Synthetase (Fad1) in Complex with Fad.
Authors: Leulliot, N. / Blondeau, K. / Keller, J. / Ulryck, N. / Quevillon-Cheruel, S. / Van Tilbeurgh, H.
History
DepositionSep 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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: FAD SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4633
Polymers35,5811
Non-polymers8822
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.871, 36.861, 79.231
Angle α, β, γ (deg.)90.00, 92.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FAD SYNTHETASE / FMN ADENYLYLTRANSFERASE / FAD PYROPHOSPHORYLASE / FLAVIN ADENINE DINUCLEOTIDE SYNTHETASE


Mass: 35581.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: P38913, FAD synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.11 % / Description: NONE
Crystal growDetails: 17 TO 25% ETHYLENE GLYCOL, 50-100MM AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22638 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 17.22 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.3 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→39.582 Å / SU ML: 0.73 / σ(F): 1.37 / Phase error: 21.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 2193 5.1 %
Rwork0.174 --
obs0.1768 21481 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.935 Å2 / ksol: 0.416 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7317 Å2-0 Å21.8915 Å2
2---3.3769 Å2-0 Å2
3----0.3548 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 58 209 2613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122470
X-RAY DIFFRACTIONf_angle_d1.3253359
X-RAY DIFFRACTIONf_dihedral_angle_d20.632886
X-RAY DIFFRACTIONf_chiral_restr0.08356
X-RAY DIFFRACTIONf_plane_restr0.006418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94130.33441450.22232593X-RAY DIFFRACTION95
1.9413-1.98650.26251260.19782521X-RAY DIFFRACTION95
1.9865-2.03610.25551200.1872599X-RAY DIFFRACTION95
2.0361-2.09120.23641270.17932565X-RAY DIFFRACTION95
2.0912-2.15270.23091260.18022565X-RAY DIFFRACTION95
2.1527-2.22220.25261530.17182502X-RAY DIFFRACTION95
2.2222-2.30160.24531280.16482618X-RAY DIFFRACTION95
2.3016-2.39380.23141480.14922508X-RAY DIFFRACTION95
2.3938-2.50270.21081340.14992577X-RAY DIFFRACTION95
2.5027-2.63460.28941430.15982576X-RAY DIFFRACTION95
2.6346-2.79960.20911410.16992505X-RAY DIFFRACTION95
2.7996-3.01570.21581520.16682549X-RAY DIFFRACTION94
3.0157-3.31910.20761390.16822520X-RAY DIFFRACTION94
3.3191-3.7990.20721340.1692520X-RAY DIFFRACTION93
3.799-4.78510.211260.1492395X-RAY DIFFRACTION89
4.7851-39.59090.20021510.18662637X-RAY DIFFRACTION97

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