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- PDB-8rom: Crystal structure of human FAD synthase PAPS domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8rom
TitleCrystal structure of human FAD synthase PAPS domain in complex with FAD
ComponentsFAD synthase
KeywordsFLAVOPROTEIN / Human FAD synthase / FAD synthesis / FAD hydrolysis / bifunctional protein
Function / homology
Function and homology information


Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / mitochondrial matrix / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
FAD synthetase with the MoaB/Mog domain / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / FAD synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsLeo, G. / Capaldi, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaPE_00000019 "HEAL ITALIA" Italy
CitationJournal: Structure / Year: 2024
Title: Structural insights into the bifunctional enzyme human FAD synthase.
Authors: Leo, G. / Leone, P. / Ataie Kachoie, E. / Tolomeo, M. / Galluccio, M. / Indiveri, C. / Barile, M. / Capaldi, S.
History
DepositionJan 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 24, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7014
Polymers22,7261
Non-polymers9753
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-20 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.959, 69.731, 105.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-706-

HOH

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Components

#1: Protein FAD synthase / FAD pyrophosphorylase / FMN adenylyltransferase / Flavin adenine dinucleotide synthase


Mass: 22725.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLAD1, PP591 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q8NFF5, FAD synthase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.6 M Na/K phosphate, pH 6, 10% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.69→58.144 Å / Num. obs: 24610 / % possible obs: 92.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 25.51 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.3
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1321 / CC1/2: 0.649 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→31.36 Å / SU ML: 0.1942 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.4193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2066 1224 4.98 %
Rwork0.1815 23373 -
obs0.1828 24597 92.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.06 Å2
Refinement stepCycle: LAST / Resolution: 1.69→31.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 63 136 1732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111638
X-RAY DIFFRACTIONf_angle_d1.19222238
X-RAY DIFFRACTIONf_chiral_restr0.053242
X-RAY DIFFRACTIONf_plane_restr0.0175278
X-RAY DIFFRACTIONf_dihedral_angle_d11.8528216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.760.31091610.28432750X-RAY DIFFRACTION99.49
1.76-1.840.27181500.23662708X-RAY DIFFRACTION97.91
1.84-1.940.27411050.2242173X-RAY DIFFRACTION77.67
1.94-2.050.241370.2092729X-RAY DIFFRACTION99.38
2.08-2.220.191340.1772409X-RAY DIFFRACTION99.1
2.22-2.440.22041300.18272446X-RAY DIFFRACTION87.35
2.44-2.790.23721130.17842628X-RAY DIFFRACTION92.32
2.79-3.520.17491430.1842773X-RAY DIFFRACTION97.14
3.52-31.360.18941510.1592757X-RAY DIFFRACTION93.24
Refinement TLS params.Method: refined / Origin x: -24.0818365529 Å / Origin y: -17.2474867873 Å / Origin z: -15.3082078726 Å
111213212223313233
T0.157493684496 Å20.0112383734662 Å20.00240328937596 Å2-0.161333909135 Å2-0.00601815637578 Å2--0.170409731396 Å2
L2.06665438722 °20.05340180028 °2-0.766875167066 °2-2.19509211458 °20.349160716927 °2--2.77193396015 °2
S0.00636358778319 Å °0.139242018382 Å °0.0483081043879 Å °-0.184913022617 Å °0.11137053665 Å °-0.187402897981 Å °0.0557150227554 Å °0.240638600235 Å °-0.0805899072439 Å °
Refinement TLS groupSelection details: all

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