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- PDB-6oxh: X-ray crystal structure of His-tagged Y140F FtmOx1 bound to Fe(II... -

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Basic information

Entry
Database: PDB / ID: 6oxh
TitleX-ray crystal structure of His-tagged Y140F FtmOx1 bound to Fe(II) and 2-oxoglutarate
ComponentsVerruculogen synthase
KeywordsOXIDOREDUCTASE / endoperoxidation / deprenylation / oxygenase / metalloenzyme / fumitremorgin / verruculogen
Function / homology
Function and homology information


verruculogen synthase / verruculogen biosynthetic process / dioxygenase activity
Similarity search - Function
q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Verruculogen synthase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsDunham, N.P. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119707 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Hydrogen Donation but not Abstraction by a Tyrosine (Y68) during Endoperoxide Installation by Verruculogen Synthase (FtmOx1).
Authors: Dunham, N.P. / Del Rio Pantoja, J.M. / Zhang, B. / Rajakovich, L.J. / Allen, B.D. / Krebs, C. / Boal, A.K. / Bollinger Jr., J.M.
History
DepositionMay 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)70,6106
Polymers70,2062
Non-polymers4044
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-52 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.512, 79.362, 91.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Verruculogen synthase / Fumitremorgin biosynthesis protein F / FtmOx1


Mass: 35103.172 Da / Num. of mol.: 2 / Mutation: Y140F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: ftmOx1, ftmF, AFUA_8G00230 / Production host: Escherichia coli (E. coli) / 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
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 35.3 % / Mosaicity: 1.342 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5 / Details: PEG4000, magnesium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 40810 / % possible obs: 98.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Χ2: 0.897 / Net I/σ(I): 7.9 / Num. measured all: 271901
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.92-1.955.70.8518920.8330.3710.930.893.7
1.95-1.995.80.72319480.8740.3110.7890.77294.7
1.99-2.036.10.65119340.8950.2760.7090.80895.4
2.03-2.076.20.55919790.9010.2360.6080.84598.2
2.07-2.116.40.49220390.9380.2060.5350.8499.4
2.11-2.166.60.42420420.9550.1760.460.86699.9
2.16-2.226.80.36720250.9670.1510.3980.906100
2.22-2.286.90.35120330.9660.1430.380.92299.9
2.28-2.346.80.2720630.9830.1110.2920.91599.6
2.34-2.426.90.22420050.9830.0920.2430.9599.6
2.42-2.516.80.19620480.9860.080.2120.95699.5
2.51-2.616.90.16420490.990.0670.1770.95299.4
2.61-2.726.90.13320520.9940.0550.1440.92799.2
2.72-2.876.90.10220320.9950.0420.110.92599.5
2.87-3.056.90.08320700.9950.0340.090.9499.6
3.05-3.2870.07120600.9950.0290.0771.05299.3
3.28-3.616.90.05820780.9960.0240.0631.10199.8
3.61-4.147.10.04421010.9980.0180.0470.878100
4.14-5.2170.03521220.9990.0140.0380.70799.5
5.21-506.60.04122380.9980.0180.0440.81299.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZON

4zon
PDB Unreleased entry


Resolution: 1.92→59.96 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.899 / SU B: 4.565 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.197
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 1679 4.7 %RANDOM
Rwork0.23 ---
obs0.2313 33672 85.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.7 Å2 / Biso mean: 25.527 Å2 / Biso min: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0 Å2
2--1.02 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.92→59.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 0 22 48 4603
Biso mean--29.02 16.96 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194663
X-RAY DIFFRACTIONr_bond_other_d0.0010.024468
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.9756347
X-RAY DIFFRACTIONr_angle_other_deg0.739310284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.923.395215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82415766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3261542
X-RAY DIFFRACTIONr_chiral_restr0.0620.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021044
LS refinement shellResolution: 1.924→1.974 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 78 -
Rwork0.254 1445 -
all-1523 -
obs--50.99 %

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