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- PDB-7etl: The crystal structure of FtmOx1-Y68F -

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Basic information

Entry
Database: PDB / ID: 7etl
TitleThe crystal structure of FtmOx1-Y68F
ComponentsVerruculogen synthase
KeywordsOXIDOREDUCTASE / non-heme iron enzyme / endoperoxide / mutant
Function / homology
Function and homology information


verruculogen synthase / verruculogen biosynthetic process / dioxygenase activity
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / : / Verruculogen synthase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99212801333 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,83811
Polymers70,1322
Non-polymers7069
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-93 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.252, 45.383, 104.963
Angle α, β, γ (deg.)90.000, 100.264, 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: 35066.023 Da / Num. of mol.: 2 / Mutation: Y68F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: ftmOx1 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q4WAW9, verruculogen synthase

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Non-polymers , 7 types, 241 molecules

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


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-tris pH 7.0, 1.9 M ammonium sulfate,0,05 M CoCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 38521 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.6288877739 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.175 / Rsym value: 0.175 / Net I/σ(I): 10.125
Reflection shellResolution: 1.99→2.02 Å / Rmerge(I) obs: 0.877 / Num. unique obs: 1881 / CC1/2: 0.539 / Rsym value: 0.877

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Processing

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

4zon
PDB Unreleased entry


Resolution: 1.99212801333→27.7054821166 Å / SU ML: 0.233602024323 / Cross valid method: FREE R-VALUE / σ(F): 1.35031747064 / Phase error: 21.5983391972
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.220241286894 1857 5.09465020576 %
Rwork0.171438149718 34593 -
obs0.173886221329 36450 94.3469482839 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.6674714723 Å2
Refinement stepCycle: LAST / Resolution: 1.99212801333→27.7054821166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 0 37 232 4841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006681780649294711
X-RAY DIFFRACTIONf_angle_d0.861674173966414
X-RAY DIFFRACTIONf_chiral_restr0.0503944281487715
X-RAY DIFFRACTIONf_plane_restr0.00594769181915848
X-RAY DIFFRACTIONf_dihedral_angle_d15.0348270692869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99213-2.0460.269664119771940.245741127521521X-RAY DIFFRACTION54.6346414073
2.046-2.10620.2844102108541290.2102388258822227X-RAY DIFFRACTION80.4644808743
2.1062-2.17410.2710786772311480.2067953876722648X-RAY DIFFRACTION95.0373895309
2.1741-2.25180.2476877383931500.198795255632751X-RAY DIFFRACTION98.6063902107
2.2518-2.34190.2341997709571650.1910638305952763X-RAY DIFFRACTION99.1198375085
2.3419-2.44840.255935569131430.1836515709422801X-RAY DIFFRACTION99.6614759648
2.4484-2.57740.2595074199551480.1776905121192792X-RAY DIFFRACTION99.9659979599
2.5774-2.73880.2469342967331480.1772204053032826X-RAY DIFFRACTION100
2.7388-2.950.2075332154261420.1727022265652827X-RAY DIFFRACTION100
2.95-3.24650.2159386558041460.1673130152922841X-RAY DIFFRACTION99.9665327979
3.2465-3.71530.2102362400851600.1607540656532825X-RAY DIFFRACTION100
3.7153-4.67720.1704141185541470.1408026327212842X-RAY DIFFRACTION99.6001332889
4.6772-27.705480.215786424741370.1701059857412929X-RAY DIFFRACTION98.9990313206

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