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- PDB-9j1h: The binary complex structure of F2Y224-FtmOx1 mutant with alpha-k... -

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Basic information

Entry
Database: PDB / ID: 9j1h
TitleThe binary complex structure of F2Y224-FtmOx1 mutant with alpha-ketoglutarate
ComponentsVerruculogen synthase
KeywordsOXIDOREDUCTASE / dioxygenase / non-heme / iron dependent
Function / homologyverruculogen synthase / verruculogen biosynthetic process / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / 2-OXOGLUTARIC ACID / : / Verruculogen synthase
Function and homology information
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,8348
Polymers70,2362
Non-polymers5986
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-72 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.032, 62.077, 151.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 426 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 100 mM Bis-Tris pH 6.4 50 mM CoCl2 1.8 M ammonium sulfate
PH range: 6.0-7.0

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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: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→47.95 Å / Num. obs: 40043 / % possible obs: 99.04 % / Redundancy: 5.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.129 / Net I/σ(I): 9.28
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.4696 / Num. unique obs: 3641 / CC1/2: 0.846 / Rrim(I) all: 0.5454

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.95 Å / Cross valid method: FREE R-VALUE / σ(F): 44.63 / Phase error: 21.3399
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1935 2009 5.02 %
Rwork0.1721 38034 -
obs0.1815 40043 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.08 Å2
Refinement stepCycle: LAST / Resolution: 2→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 33 420 4919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074599
X-RAY DIFFRACTIONf_angle_d0.94116261
X-RAY DIFFRACTIONf_chiral_restr0.0515699
X-RAY DIFFRACTIONf_plane_restr0.016827
X-RAY DIFFRACTIONf_dihedral_angle_d15.07891757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.291260.26482376X-RAY DIFFRACTION84.46
2.05-2.10.29191370.24362608X-RAY DIFFRACTION91.57
2.1-2.160.27671410.23392674X-RAY DIFFRACTION94.59
2.16-2.230.24321450.2292757X-RAY DIFFRACTION95
2.23-2.310.27741420.23422703X-RAY DIFFRACTION94.98
2.31-2.40.22491430.2342710X-RAY DIFFRACTION94.95
2.4-2.510.23021430.22212718X-RAY DIFFRACTION94.97
2.51-2.650.24081420.2152711X-RAY DIFFRACTION94.99
2.65-2.810.24341460.20842770X-RAY DIFFRACTION94.96
2.81-3.030.22271440.19482728X-RAY DIFFRACTION94.92
3.03-3.330.19921440.16572753X-RAY DIFFRACTION95
3.33-3.820.16531470.14722778X-RAY DIFFRACTION94.91
3.82-4.810.1461480.12872815X-RAY DIFFRACTION94.91
4.81-47.950.18111550.16182939X-RAY DIFFRACTION94.84
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)
12.596748502390.6021133435280.4805706595412.129545971080.09281221937111.63886394913-0.07981695527640.121543506418-0.162427662791-0.3172305539810.0381991216015-0.1824117070840.1639385557420.05814503212550.04322858029290.2549040950990.05646843303290.01432356475320.12034451513-0.03144113511620.32491867976836.878291173-11.44706321177.79701308199
20.498108964797-0.611061931423-0.5937033111481.67279659752-1.633042181236.715641170960.0378076644469-0.0803001204851-0.06525067184340.0430980889741-0.0287711445982-0.132663012764-0.0558065486040.163774778316-0.0152116158280.133542866846-0.0320500007727-0.01111084211760.163711257120.01800664246860.33403457905539.8253371756-1.4345112278720.6131661057
30.6722853328410.400713363789-0.145439713922.23020822882-0.2651450692270.9867723647030.0238190931006-0.0864740365391-0.238238940546-0.1217775264760.0134572327368-0.02905201668780.206884230271-0.0099913933888-0.04984807784490.223016105626-0.0196156738479-0.04593559306290.1409360153240.01286522367220.36951359765528.4085774567-9.924677805715.307275557
42.564212807592.94970713294-0.7006567010043.64590001242-0.5503079180161.804544175550.162482400964-0.446592142270.06396327879410.2391358957550.131224495225-0.08713341653240.3200467483560.00127115023304-0.2528100237150.4959794507610.0141700946235-0.03594651366680.1716792881720.07704669609970.37068789521323.6146811489-23.311052145221.4303853957
51.629743849370.626321059869-0.08534166469972.50076321705-0.9456725445131.63527255279-0.0908308894060.210490759991-0.00785866403149-0.01222292885050.0299202384897-0.3526472568780.3403244788310.09343011956380.04129975849190.3098612221160.019633819123-0.04246714615930.123219879065-0.03612640664190.39366731603731.6489422538-15.112718269912.9740897892
60.66403739209-0.927640687295-0.06384180526472.323106666-0.3268192308971.352077757460.123292799658-0.020750807306-0.188544419064-0.169176913685-0.00877647621652-0.04138748798240.07289776620860.00244112339301-0.1114472476680.149075241953-0.0367462219662-0.02489050719490.132732855771-0.009890915900990.27147935743832.66583768693.1789275197513.349849299
72.65612252542-0.0473609199751-1.820457904622.47453648281-0.04523499933023.899879016410.2163373399510.0170562153550.514661800208-0.196027962107-0.110605349041-0.118081159955-0.3889586677490.0985537867997-0.1117780706860.204689964916-0.0117900984138-0.02270157097250.1359140527330.04146510405660.34030752975727.81540470318.6781639447.91972525649
83.16084870990.54118673193-0.2617314165641.723993539280.1766026625441.080805726790.0433443572568-0.4933209048450.1930446178220.263643284256-0.01486210161450.460281729613-0.108318204113-0.224522139267-0.007171750503230.186623875940.04229945382650.05123165167060.3062673464560.01442574813380.3448940004233.2278321692520.482226712731.4520576591
90.404709813233-0.0733584359863-0.3591850531544.675053818572.225363092611.316586347580.5912388858390.3258293842570.5279854414150.320919366062-0.6754896857080.332179796904-0.595255481677-0.5494133995290.08710144336590.7703422043420.106894722628-0.1356146065670.479015554004-0.08098690036740.45248308257115.970306379626.4949010285.87778172001
104.121324161611.6168663321.813492630840.6625127581970.9705108535593.167200642890.04057134562910.816457330972-0.24930662287-0.542953149464-0.0551479501332-0.1100368212540.1048059341270.5277648276760.04515320085431.01819828497-0.1550472688680.4600567931290.574181125578-0.1941899056790.627839719756.9423480390128.79813776257.41240724281
111.94163714118-0.932542195152-0.06077841784032.31386009017-0.5655696284311.94366301312-0.0182687997723-0.2517607459170.006123766334810.01391020198610.08431871558160.0605119815619-0.0340062890619-0.124424203206-0.07193006950020.0819665410219-0.0105584333345-0.00641894716730.203222386905-0.006918917305790.26517875033113.903274857118.428075822426.6147130309
122.242833366320.2252568707950.1075738888740.407088994805-0.1620562305390.7625711931860.01744274089280.110982613735-0.085606114808-0.09971933107580.04791277619330.1552084265360.00644534598886-0.229998782006-0.04978188312640.154578934812-0.0228440335711-0.01510437058030.2873249273540.07681121045830.4080472813160.29415928977112.773051072120.2551722431
135.13519575772-3.171032572592.20554279515.65829022849-0.1112632816672.1904182412-0.02142241704580.09599384086090.452281501383-0.465364560956-0.4088024788320.415076904563-0.25464896112-0.1578431937730.2574702085590.362113586170.214315269830.1222963573880.7736079114680.5210681072410.984349227409-6.3582851747732.341094516314.3632096554
141.62294204856-0.9595520998890.3517220306562.00189094356-0.1535221198220.858111879808-0.0429070434601-0.2976368318740.01623637587010.02952871758510.114623987597-0.0407920733184-0.05861090455060.049071277361-0.06745199721770.12529134167-0.01820724207650.003943967344050.20297817801-0.005760060073730.26312820948725.032804661814.448970016726.6432644765
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 6:58)AA6 - 581 - 53
22(chain A and resid 59:93)AA59 - 9354 - 88
33(chain A and resid 94:174)AA94 - 17489 - 169
44(chain A and resid 175:188)AA175 - 188170 - 183
55(chain A and resid 189:209)AA189 - 209184 - 204
66(chain A and resid 210:268)AA210 - 268205 - 263
77(chain A and resid 269:289)AA269 - 289264 - 284
88(chain B and resid 6:54)BF6 - 541 - 49
99(chain B and resid 55:68)BF55 - 6850 - 63
1010(chain B and resid 69:73)BF69 - 7364 - 65
1111(chain B and resid 74:120)BF74 - 12066 - 112
1212(chain B and resid 121:208)BF121 - 208113 - 200
1313(chain B and resid 209:216)BF209 - 216201 - 208
1414(chain B and resid 217:289)BF217 - 289209 - 281

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