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- PDB-9j1i: Apo structure of the F2Y224-FtmOx1 mutant with metal Iron -

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Basic information

Entry
Database: PDB / ID: 9j1i
TitleApo structure of the F2Y224-FtmOx1 mutant with metal Iron
ComponentsVerruculogen synthase
KeywordsOXIDOREDUCTASE / dioxygenase / non-heme / iron dependent
Function / homologyverruculogen synthase / verruculogen biosynthetic process / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / : / : / Verruculogen synthase
Function and homology information
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsWang, X.Y. / Wang, J. / Yan, W.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Catalysis Science And Technology / Year: 2025
Title: Characterizing Y224 conformational flexibility in FtmOx1-catalysis using 19 F NMR spectroscopy.
Authors: Wang, X. / Yang, L. / Wang, S. / Wang, J. / Li, K. / Naowarojna, N. / Ju, Y. / Ye, K. / Han, Y. / Yan, W. / Liu, X. / Zhang, L. / Liu, P.
History
DepositionAug 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Verruculogen synthase
B: Verruculogen synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4075
Polymers70,2362
Non-polymers1713
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-57 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.443, 45.610, 105.148
Angle α, β, γ (deg.)90.000, 100.020, 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

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Components

#1: Protein Verruculogen synthase / Fumitremorgin biosynthesis protein F


Mass: 35118.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: ftmOx1, ftmF, AFUA_8G00230 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4WAW9, verruculogen synthase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.23 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES pH 6.0 50 mM CoCl2 1.8 M ammonium sulfate
PH range: 5.6-6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.11→36.08 Å / Num. obs: 32539 / % possible obs: 99.19 % / Redundancy: 3.2 % / Biso Wilson estimate: 35.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0691 / Rrim(I) all: 0.083 / Net I/σ(I): 11.18
Reflection shellResolution: 2.11→2.19 Å / Num. unique obs: 3155 / CC1/2: 0.686

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y5S

4y5s


Resolution: 2.11→36.08 Å / SU ML: 0.2472 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2159 1627 5 %
Rwork0.1722 30904 -
obs0.1744 32531 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.85 Å2
Refinement stepCycle: LAST / Resolution: 2.11→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4501 0 3 222 4726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744612
X-RAY DIFFRACTIONf_angle_d0.85276286
X-RAY DIFFRACTIONf_chiral_restr0.0517703
X-RAY DIFFRACTIONf_plane_restr0.0081830
X-RAY DIFFRACTIONf_dihedral_angle_d14.00771762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.170.29931310.24032497X-RAY DIFFRACTION96.83
2.17-2.240.28091350.22192564X-RAY DIFFRACTION99.56
2.24-2.330.24821350.20262557X-RAY DIFFRACTION99.81
2.33-2.420.25941350.19122566X-RAY DIFFRACTION99.63
2.42-2.530.24871350.19062582X-RAY DIFFRACTION99.67
2.53-2.660.25461350.19562555X-RAY DIFFRACTION99.78
2.66-2.830.24871350.1912573X-RAY DIFFRACTION99.74
2.83-3.050.23991370.19252586X-RAY DIFFRACTION99.27
3.05-3.350.23971340.17552554X-RAY DIFFRACTION99.22
3.35-3.840.20011370.15622606X-RAY DIFFRACTION99.31
3.84-4.830.16221370.13222602X-RAY DIFFRACTION99.2
4.83-36.080.19181410.16892662X-RAY DIFFRACTION98.28
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.895136572930.9025655166730.5242679845022.84344150244-0.9819177605093.85467370609-0.1242148203360.4357659386240.2060525829140.0137762769610.0290857478576-0.423823285274-0.4385537165560.8818909733290.05010448376310.416998658284-0.04784031818180.1141512240630.587617411741-0.1273525943320.3858848922741.70213.739-46.019
20.2890901636120.326708965274-0.7682081458150.354713588818-0.8555382229762.089228749630.6012923871670.259046582457-0.72753720144-0.754285111956-0.133249879437-0.1870485451330.109179956206-0.650486955611-0.4196619560550.6221120233310.184753554028-0.01305267411790.715690921734-0.1577913312451.10579997466-1.986-12.55-32.065
38.97992832332-0.200639795891-3.512346394786.188642690110.4661434806547.03183575513-0.9133244607621.49851641607-0.930719100813-0.3900418496060.0416554842089-0.4270879513940.818492254782-0.2048865721620.8565463990790.857104232223-0.07157746275140.05661126886060.570786343348-0.1383531510280.671843584327-13.456-10.005-37.638
42.10169999494-0.2841446606620.4223206153241.088361065750.1587428467182.387982490580.01446898349120.145573549737-0.253508946181-0.1204852793920.0647467226687-0.175703944060.1288511967210.171127726643-0.07493322283210.264795451049-0.0195268206660.05598538206230.281769098813-0.03452610704120.294133497714-9.2459.236-38.475
52.752094037781.078285788282.400414073611.60126618501-0.5734045290144.051589247490.03551145873290.345674627257-0.252736976493-0.3008172461780.115740495685-0.209151867601-0.006568108216890.473263539923-0.150982864060.381522822668-0.006874148230440.06596894154820.431984691332-0.07957891571830.273814279764-8.1658.652-52.023
61.77634394044-0.2674981594580.09977528069632.142852768710.4791981607733.06684478203-0.04691323247610.101474174855-0.231884167032-0.04179356690950.0581812488503-0.1276545535640.08566279766860.2693348775510.00652534022180.211404063836-0.01427564419460.03072985499640.213625114426-0.03756942841040.297389117776-7.5379.184-29.729
72.62992957898-1.48857684505-2.614141584282.124351655541.164878605973.10892880581-0.043404835273-0.9404827319340.9606330449250.3512113261660.319703226219-0.273308152373-0.239816788330.493947617077-0.2644807767820.3220616967250.0290071587913-0.07481473407450.437178526169-0.05839253789430.379793282124-4.95516.343-14.228
84.87742581060.1814377269321.853671480051.2616174878-0.6846016723833.70509844681-0.046912099372-0.194989758635-0.2839384172880.06884475956690.04040044740930.236958850650.112259086574-0.621738863182-0.00911555508090.290423835857-0.001770686807910.05875524915950.278626650702-0.05401690289850.353174651669-40.61713.67-14.331
96.860570406860.707381286057-3.387078818534.090833045191.605988457092.641767428740.786228799672-0.7717140495680.97771513603-0.1327556948240.119089019963-0.187126161913-0.6587775612230.318772799629-0.8540198408050.525184582742-0.01933902396420.09998163374080.410192738204-0.0618102853320.500747257605-19.49427.025-9.185
101.56921576778-0.6398902442510.1582482616221.535117586-0.1214435236221.83942356221-0.03581770310380.0130374030368-0.01582429633080.0488935047130.008035295177780.107346512995-0.0316486536337-0.1670413429030.02352287278450.235781105326-0.02639275516370.0164830558560.24976529395-0.003344173751450.284580923246-30.72715.055-21.289
113.73771962439-1.184488530970.7887238428893.58151968822-0.5217446217784.68118168150.00117163468627-0.05425368295320.2920746034180.02116943818660.05714011456040.149435230319-0.418224745467-0.137778920659-0.06402530954050.2017955576090.00215356740076-0.007545693116760.264889115784-0.04717366161730.310332265684-40.82824.262-20.899
123.06080864791-2.37379645843-1.362006807126.056383737013.459892058193.70964294208-0.180655217258-0.2745255706630.4368090344220.09004685743260.01465497912310.0945373586571-0.222270631020.03123142421330.1471225984250.276610559735-0.00180319154455-0.03404098693150.294884521005-0.0507653235670.338452824879-35.60324.832-9.724
131.707074985480.7168413434441.30847599631.11580753659-0.4205973883664.508098202690.0775178473487-0.319658391597-0.03254357553490.3468612725850.08375918257890.0943444320314-0.165604616664-0.318009468287-0.1485880482950.2735863472410.016378952157-0.001624273352760.225004223046-0.02245737348470.304556162835-19.2689.193-19.169
143.20685145332-1.05844627177-0.526254042.9834885799-0.01500754341434.62069942696-0.0203932037553-0.0402184068668-0.4415789991030.01667191372750.02840192275760.013877543150.5017242731970.225717413061-0.0006537383128010.321654930979-0.0293014597282-0.02307359346660.201101717239-0.02779647272670.386599188271-20.142-2.095-21.173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:50 )A6 - 50
2X-RAY DIFFRACTION2( CHAIN A AND RESID 51:59 )A51 - 59
3X-RAY DIFFRACTION3( CHAIN A AND RESID 60:72 )A60 - 72
4X-RAY DIFFRACTION4( CHAIN A AND RESID 73:150 )A73 - 150
5X-RAY DIFFRACTION5( CHAIN A AND RESID 151:206 )A151 - 206
6X-RAY DIFFRACTION6( CHAIN A AND RESID 207:274 )A207 - 274
7X-RAY DIFFRACTION7( CHAIN A AND RESID 275:289 )A275 - 289
8X-RAY DIFFRACTION8( CHAIN B AND RESID 6:57 )B6 - 57
9X-RAY DIFFRACTION9( CHAIN B AND RESID 58:76 )B58 - 76
10X-RAY DIFFRACTION10( CHAIN B AND RESID 77:150 )B77 - 150
11X-RAY DIFFRACTION11( CHAIN B AND RESID 151:209 )B151 - 209
12X-RAY DIFFRACTION12( CHAIN B AND RESID 210:225 )B210 - 225
13X-RAY DIFFRACTION13( CHAIN B AND RESID 226:241 )B226 - 241
14X-RAY DIFFRACTION14( CHAIN B AND RESID 242:290 )B242 - 290

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