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- PDB-8ron: Crystal structure of human FAD synthase, isoform 2 -

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Basic information

Entry
Database: PDB / ID: 8ron
TitleCrystal structure of human FAD synthase, isoform 2
ComponentsIsoform 2 of FAD 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 / : / FAD synthase, middle domain / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase domain / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of FAD synthase
B: Isoform 2 of FAD synthase
C: Isoform 2 of FAD synthase
D: Isoform 2 of FAD synthase


Theoretical massNumber of molelcules
Total (without water)213,5264
Polymers213,5264
Non-polymers00
Water00
1
A: Isoform 2 of FAD synthase
B: Isoform 2 of FAD synthase


Theoretical massNumber of molelcules
Total (without water)106,7632
Polymers106,7632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Isoform 2 of FAD synthase
D: Isoform 2 of FAD synthase


Theoretical massNumber of molelcules
Total (without water)106,7632
Polymers106,7632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.754, 187.740, 79.383
Angle α, β, γ (deg.)90.000, 96.453, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 110 through 147 or resid 149...
d_2ens_1(chain "B" and (resid 110 through 147 or resid 149...
d_3ens_1(chain "C" and (resid 110 through 147 or resid 149...
d_4ens_1(chain "D" and (resid 110 through 147 or resid 149...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERCYSCYSAA110 - 1475 - 42
d_12VALVALPROPROAA149 - 20344 - 98
d_13LEULEUGLYGLYAA205 - 232100 - 127
d_14ASPASPPHEPHEAA234 - 241129 - 136
d_15PHEPHEVALVALAA243 - 248138 - 143
d_16ASNASNPROPROAA250 - 258145 - 153
d_17LEULEUSERSERAA260 - 281155 - 176
d_18GLUGLUGLYGLYAA283 - 305178 - 200
d_19ARGARGALAALAAA307 - 344202 - 239
d_110LEULEUPROPROAA346 - 356241 - 251
d_111ALAALAGLNGLNAA362 - 421257 - 316
d_112LYSLYSLYSLYSAA423318
d_113PROPROPROPROAA425320
d_114PROPROPROPROAA428323
d_115PROPROARGARGAA430 - 437325 - 332
d_116SERSERLEULEUAA440 - 445335 - 340
d_117GLNGLNILEILEAA447 - 453342 - 348
d_118TYRTYRLEULEUAA456 - 458351 - 353
d_119METMETLEULEUAA460 - 461355 - 356
d_120ALAALALEULEUAA463 - 474358 - 369
d_121ALAALAPROPROAA476 - 479371 - 374
d_122LEULEUTHRTHRAA481 - 491376 - 386
d_123PROPROPROPROAA493388
d_124SERSERSERSERAA495 - 549390 - 444
d_125ASNASNVALVALAA552 - 554447 - 449
d_126ASNASNASNASNAA556451
d_127PROPROGLUGLUAA572 - 577467 - 472
d_21SERSERCYSCYSBB110 - 1475 - 42
d_22VALVALPROPROBB149 - 20344 - 98
d_23LEULEUGLYGLYBB205 - 232100 - 127
d_24ASPASPPHEPHEBB234 - 241129 - 136
d_25PHEPHEVALVALBB243 - 248138 - 143
d_26ASNASNPROPROBB250 - 258145 - 153
d_27LEULEUSERSERBB260 - 281155 - 176
d_28GLUGLUGLYGLYBB283 - 305178 - 200
d_29ARGARGALAALABB307 - 344202 - 239
d_210LEULEUPROPROBB346 - 356241 - 251
d_211ALAALAGLNGLNBB362 - 421257 - 316
d_212LYSLYSLYSLYSBB423318
d_213PROPROPROPROBB425320
d_214PROPROPROPROBB428323
d_215PROPROARGARGBB430 - 437325 - 332
d_216SERSERLEULEUBB440 - 445335 - 340
d_217GLNGLNILEILEBB447 - 453342 - 348
d_218TYRTYRLEULEUBB456 - 458351 - 353
d_219METMETLEULEUBB460 - 461355 - 356
d_220ALAALALEULEUBB463 - 474358 - 369
d_221ALAALAPROPROBB476 - 479371 - 374
d_222LEULEUTHRTHRBB481 - 491376 - 386
d_223PROPROPROPROBB493388
d_224SERSERSERSERBB495 - 549390 - 444
d_225ASNASNVALVALBB552 - 554447 - 449
d_226ASNASNASNASNBB556451
d_227PROPROGLUGLUBB572 - 577467 - 472
d_31SERSERCYSCYSCC110 - 1475 - 42
d_32VALVALPROPROCC149 - 20344 - 98
d_33LEULEUGLYGLYCC205 - 232100 - 127
d_34ASPASPPHEPHECC234 - 241129 - 136
d_35PHEPHEVALVALCC243 - 248138 - 143
d_36ASNASNPROPROCC250 - 258145 - 153
d_37LEULEUSERSERCC260 - 281155 - 176
d_38GLUGLUGLYGLYCC283 - 305178 - 200
d_39ARGARGALAALACC307 - 344202 - 239
d_310LEULEUPROPROCC346 - 356241 - 251
d_311ALAALAGLNGLNCC362 - 421257 - 316
d_312LYSLYSLYSLYSCC423318
d_313PROPROPROPROCC425320
d_314PROPROPROPROCC428323
d_315PROPROARGARGCC430 - 437325 - 332
d_316SERSERLEULEUCC440 - 445335 - 340
d_317GLNGLNILEILECC447 - 453342 - 348
d_318TYRTYRLEULEUCC456 - 458351 - 353
d_319METMETLEULEUCC460 - 461355 - 356
d_320ALAALALEULEUCC463 - 474358 - 369
d_321ALAALAPROPROCC476 - 479371 - 374
d_322LEULEUTHRTHRCC481 - 491376 - 386
d_323PROPROPROPROCC493388
d_324SERSERSERSERCC495 - 549390 - 444
d_325ASNASNVALVALCC552 - 554447 - 449
d_326ASNASNASNASNCC556451
d_327PROPROGLUGLUCC572 - 577467 - 472
d_41SERSERCYSCYSDD110 - 1475 - 42
d_42VALVALPROPRODD149 - 20344 - 98
d_43LEULEUGLYGLYDD205 - 232100 - 127
d_44ASPASPPHEPHEDD234 - 241129 - 136
d_45PHEPHEVALVALDD243 - 248138 - 143
d_46ASNASNPROPRODD250 - 258145 - 153
d_47LEULEUSERSERDD260 - 281155 - 176
d_48GLUGLUGLYGLYDD283 - 305178 - 200
d_49ARGARGALAALADD307 - 344202 - 239
d_410LEULEUPROPRODD346 - 356241 - 251
d_411ALAALAGLNGLNDD362 - 421257 - 316
d_412LYSLYSLYSLYSDD423318
d_413PROPROPROPRODD425320
d_414PROPROPROPRODD428323
d_415PROPROARGARGDD430 - 437325 - 332
d_416SERSERLEULEUDD440 - 445335 - 340
d_417GLNGLNILEILEDD447 - 453342 - 348
d_418TYRTYRLEULEUDD456 - 458351 - 353
d_419METMETLEULEUDD460 - 461355 - 356
d_420ALAALALEULEUDD463 - 474358 - 369
d_421ALAALAPROPRODD476 - 479371 - 374
d_422LEULEUTHRTHRDD481 - 491376 - 386
d_423PROPROPROPRODD493388
d_424SERSERSERSERDD495 - 549390 - 444
d_425ASNASNVALVALDD552 - 554447 - 449
d_426ASNASNASNASNDD556451
d_427PROPROGLUGLUDD572 - 577467 - 472

NCS oper:
IDCodeMatrixVector
1given(0.178128542442, 0.981039655806, -0.0763637093306), (0.980895741124, -0.18319637578, -0.0654418287178), (-0.0781905839111, -0.0632477796946, -0.994930123653)-8.34977682775, 14.4983429023, 55.6531808058
2given(0.999448641446, 0.00920488692125, -0.0319011468296), (0.0130003434287, -0.992580570796, 0.120891693466), (-0.0305516641611, -0.121239764661, -0.992152969699)38.288157069, 75.6151499309, 76.2090351707
3given(0.219256630037, 0.97351918686, -0.0647064370857), (-0.973580227869, 0.213970455158, -0.0797382230888), (-0.0637814243082, 0.0804800418421, 0.994713472704)28.6781313504, 67.2277033113, 18.5557465167

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Components

#1: Protein
Isoform 2 of FAD synthase / FAD pyrophosphorylase / FMN adenylyltransferase / Flavin adenine dinucleotide synthase


Mass: 53381.531 Da / Num. of mol.: 4
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
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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 10% PEG 8000 and 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.488→58.725 Å / Num. obs: 43831 / % possible obs: 93.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 59.52 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.8
Reflection shellResolution: 2.488→2.792 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2192 / CC1/2: 0.485 / % possible all: 71.3

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→58.72 Å / SU ML: 0.3993 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.5638
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2683 2155 4.96 %
Rwork0.2154 41277 -
obs0.2181 43432 64.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.99 Å2
Refinement stepCycle: LAST / Resolution: 2.6→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14498 0 0 0 14498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005814853
X-RAY DIFFRACTIONf_angle_d0.824520215
X-RAY DIFFRACTIONf_chiral_restr0.04692250
X-RAY DIFFRACTIONf_plane_restr0.00762642
X-RAY DIFFRACTIONf_dihedral_angle_d12.82485466
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.55325567075
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.20240406467
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.34626552588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID
2.6-2.660.4702130.3348357X-RAY DIFFRACTION
2.66-2.730.4136350.3401603X-RAY DIFFRACTION
2.73-2.80.3408530.3338885X-RAY DIFFRACTION
2.8-2.880.4153640.30261081X-RAY DIFFRACTION
2.88-2.980.3654750.29621391X-RAY DIFFRACTION
2.98-3.080.2814810.29661830X-RAY DIFFRACTION
3.08-3.210.31191520.30022519X-RAY DIFFRACTION
3.21-3.350.35711680.2783119X-RAY DIFFRACTION
3.35-3.530.32521870.27173746X-RAY DIFFRACTION
3.53-3.750.32822450.24384269X-RAY DIFFRACTION
3.75-4.040.25852010.21874285X-RAY DIFFRACTION
4.04-4.450.2362370.19324298X-RAY DIFFRACTION
4.45-5.090.24142240.16844261X-RAY DIFFRACTION
5.09-6.410.26262210.20864299X-RAY DIFFRACTION
6.41-58.720.21621990.18064334X-RAY DIFFRACTION
Refinement TLS params.Method: refined / Origin x: 25.8924173479 Å / Origin y: 39.6506503279 Å / Origin z: 37.2705202522 Å
111213212223313233
T0.273129159362 Å20.0481954376483 Å20.0137742349017 Å2-0.29355024935 Å2-0.0423014608108 Å2--0.359488852185 Å2
L1.13433504878 °20.298591876294 °2-0.165899935502 °2-0.556359007203 °2-0.169116986684 °2--0.381231294624 °2
S-0.0976788892549 Å °0.0708101135783 Å °-0.0950087002831 Å °0.00299835537219 Å °0.13469656056 Å °0.0313509908978 Å °-0.0204254697126 Å °-0.0588817247747 Å °-0.0197224921274 Å °
Refinement TLS groupSelection details: all

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