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- PDB-7etk: The complex structure of FtmOx1 bond with fumitremorgen B at 1.22... -

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Basic information

Entry
Database: PDB / ID: 7etk
TitleThe complex structure of FtmOx1 bond with fumitremorgen B at 1.22 angstrom
ComponentsVerruculogen synthase
KeywordsOXIDOREDUCTASE / complex / FtmOx1 / fumitremorgen B
Function / homologyverruculogen synthase / verruculogen biosynthetic process / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / fumitremorgen B / 2-OXOGLUTARIC ACID / : / Verruculogen synthase
Function and homology information
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22027438779 Å
AuthorsZhou, J.H. / Wu, L.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1.
Authors: Wu, L. / Wang, Z. / Cen, Y. / Wang, B. / Zhou, J.
History
DepositionMay 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)72,00915
Polymers70,1642
Non-polymers1,84513
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-58 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.024, 77.782, 62.208
Angle α, β, γ (deg.)90.000, 103.708, 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

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Protein , 1 types, 2 molecules AB

#1: Protein Verruculogen synthase / Fumitremorgin biosynthesis protein F


Mass: 35082.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Production host: Escherichia coli B (bacteria) / References: UniProt: Q4WAW9, verruculogen synthase

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Non-polymers , 6 types, 516 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-4Q1 / fumitremorgen B / (5aR,6S,12S,14aS)-5a,6-dihydroxy-9-methoxy-11-(3-methylbut-2-en-1-yl)-12-(2-methylprop-1-en-1-yl)-1,2,3,5a,6,11,12,14a- octahydro-5H,14H-pyrrolo[1'',2'':4',5']pyrazino[1',2':1,6]pyrido[3,4-b]indole-5,14-dione


Mass: 479.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N3O5
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-tris pH 7.0, 1.8 M Ammonium sulfate and 0.1 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 168451 / % possible obs: 99.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.950533938 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 26.95
Reflection shellResolution: 1.22→1.24 Å / Num. unique obs: 7861 / CC1/2: 0.833

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZON

4zon
PDB Unreleased entry


Resolution: 1.22027438779→30.2180349605 Å / SU ML: 0.103925944078 / Cross valid method: FREE R-VALUE / σ(F): 1.35405927813 / Phase error: 17.1346224084
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.172045210861 7924 5.13638249326 %
Rwork0.150430529054 146348 -
obs0.15155900346 154272 90.7562431979 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.4714557258 Å2
Refinement stepCycle: LAST / Resolution: 1.22027438779→30.2180349605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 118 503 5115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00728685990434870
X-RAY DIFFRACTIONf_angle_d1.083757846846668
X-RAY DIFFRACTIONf_chiral_restr0.084387976866737
X-RAY DIFFRACTIONf_plane_restr0.00664667149074879
X-RAY DIFFRACTIONf_dihedral_angle_d22.70687351051873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2203-1.23410.2296553856071410.1952734548242565X-RAY DIFFRACTION48.1409001957
1.2341-1.24870.2065912135731840.1757767456353003X-RAY DIFFRACTION56.5371651588
1.2487-1.26390.1972394833791650.1701481224693365X-RAY DIFFRACTION62.1369477205
1.2639-1.27990.1819633497851960.1676869371193609X-RAY DIFFRACTION67.8737067428
1.2799-1.29670.2031211702092130.1632037797833882X-RAY DIFFRACTION72.0950704225
1.2967-1.31450.1892310186752630.1572998144444065X-RAY DIFFRACTION76.9012082445
1.3145-1.33330.1756080955642110.1593037632354310X-RAY DIFFRACTION80.6026029595
1.3333-1.35320.1915331184322660.1592899713284412X-RAY DIFFRACTION82.1566561293
1.3532-1.37430.1985224498372750.1551429276954691X-RAY DIFFRACTION88.1903747114
1.3743-1.39680.1971203036622830.1498519144095168X-RAY DIFFRACTION96.3414634146
1.3968-1.42090.166204374362810.1424487324595342X-RAY DIFFRACTION98.7183988764
1.4209-1.44680.1858759528633080.1372900401455317X-RAY DIFFRACTION99.5399044417
1.4468-1.47460.1711301288632810.1374111392345317X-RAY DIFFRACTION99.8394863563
1.4746-1.50470.165073776892750.1349672139795378X-RAY DIFFRACTION99.6474528468
1.5047-1.53740.1946302696032450.1345582097495373X-RAY DIFFRACTION99.7160099397
1.5374-1.57320.1662898928912790.1310228602555288X-RAY DIFFRACTION98.8458806818
1.5732-1.61250.1644102473952630.1246419348955359X-RAY DIFFRACTION99.0660792952
1.6125-1.65610.1583563598012790.1279497227245399X-RAY DIFFRACTION99.9296022527
1.6561-1.70480.1555699323142510.133924161525394X-RAY DIFFRACTION99.9822883457
1.7048-1.75990.1709527907972840.1357471709185374X-RAY DIFFRACTION99.8235709245
1.7599-1.82280.1674800614912740.138271696575400X-RAY DIFFRACTION99.9823788546
1.8228-1.89570.1641803901552980.1379183103515325X-RAY DIFFRACTION99.6455785929
1.8957-1.9820.1643567671382580.140778292465368X-RAY DIFFRACTION98.7710674157
1.982-2.08650.1574359885423110.1368500677585344X-RAY DIFFRACTION99.8058595129
2.0865-2.21710.1536929428472950.1407798460515403X-RAY DIFFRACTION99.8773006135
2.2171-2.38830.1660536093953200.1475082184825349X-RAY DIFFRACTION99.8590805003
2.3883-2.62850.1763699365552910.1592222496245370X-RAY DIFFRACTION99.858881637
2.6285-3.00850.1904887420092950.1692123717415336X-RAY DIFFRACTION98.9457037428
3.0085-3.78930.1612806220323360.153389745925398X-RAY DIFFRACTION99.8606757227
3.7893-30.2180.184509254153030.167191953545444X-RAY DIFFRACTION99.1032936713

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