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- PDB-4y5s: Structure of FtmOx1 with a-Ketoglutarate as co-substrate -

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Basic information

Entry
Database: PDB / ID: 4y5s
TitleStructure of FtmOx1 with a-Ketoglutarate as co-substrate
ComponentsVerruculogen synthase
KeywordsOXIDOREDUCTASE / Complex / a-Ketoglutarate / FtmOx1
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 / Resolution: 2.543 Å
AuthorsYan, W. / Zhang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM093903 United States
CitationJournal: Nature / Year: 2015
Title: Endoperoxide formation by an alpha-ketoglutarate-dependent mononuclear non-haem iron enzyme.
Authors: Yan, W. / Song, H. / Song, F. / Guo, Y. / Wu, C.H. / Sae Her, A. / Pu, Y. / Wang, S. / Naowarojna, N. / Weitz, A. / Hendrich, M.P. / Costello, C.E. / Zhang, L. / Liu, P. / Jessie Zhang, Y.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)71,2257
Polymers70,7632
Non-polymers4635
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-61 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.532, 45.659, 105.201
Angle α, β, γ (deg.)90.00, 99.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Verruculogen synthase / Fumitremorgin biosynthesis protein F


Mass: 35381.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: ftmOx1, ftmF, AFUA_8G00230
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q4WAW9, verruculogen synthase
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES pH6.5, 50 mM CoCl2, and 2 M of ammonium sulfate
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: Si single crystal (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.543→36.13 Å / Num. obs: 18963 / % possible obs: 99.93 % / Redundancy: 3.7 % / Rsym value: 0.125 / Net I/σ(I): 10.529
Reflection shellResolution: 2.543→2.634 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.5 / % possible all: 99.35

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.543→36.126 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1867 5.13 %
Rwork0.1756 --
obs0.1785 36389 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.543→36.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4535 0 23 146 4704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174684
X-RAY DIFFRACTIONf_angle_d0.9256353
X-RAY DIFFRACTIONf_dihedral_angle_d14.5491767
X-RAY DIFFRACTIONf_chiral_restr0.037709
X-RAY DIFFRACTIONf_plane_restr0.006843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5428-2.61150.30421380.23332594X-RAY DIFFRACTION99
2.6115-2.68830.3311360.22022683X-RAY DIFFRACTION100
2.6883-2.77510.30781750.21722593X-RAY DIFFRACTION100
2.7751-2.87420.28111490.20992700X-RAY DIFFRACTION100
2.8742-2.98930.28241530.20632619X-RAY DIFFRACTION100
2.9893-3.12520.29291270.20312665X-RAY DIFFRACTION100
3.1252-3.28990.26211580.20952678X-RAY DIFFRACTION100
3.2899-3.49590.27461340.18512670X-RAY DIFFRACTION100
3.4959-3.76550.2271210.18752695X-RAY DIFFRACTION100
3.7655-4.1440.20361360.15112662X-RAY DIFFRACTION100
4.144-4.74250.15371290.12592659X-RAY DIFFRACTION100
4.7425-5.97060.19151460.15072669X-RAY DIFFRACTION100
5.9706-36.12960.2021650.15922635X-RAY DIFFRACTION100

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