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- PDB-6foq: The crystal structure of EncM complexed with dioxygen under 15 ba... -

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Basic information

Entry
Database: PDB / ID: 6foq
TitleThe crystal structure of EncM complexed with dioxygen under 15 bar of oxygen pressure.
ComponentsPutative FAD-dependent oxygenase EncM
KeywordsFLAVOPROTEIN / monooxygenase / flavin-N5-oxide / FAD / EncM / oxygenating species / oxygen binding
Function / homology
Function and homology information


FAD binding / oxidoreductase activity / identical protein binding
Similarity search - Function
: / Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 ...: / Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / OXYGEN MOLECULE / Putative FAD-dependent oxygenase EncM
Similarity search - Component
Biological speciesStreptomyces maritimus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.386 Å
AuthorsSaleem-Batcha, R. / Teufel, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationTE 931/2-1 Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Enzymatic control of dioxygen binding and functionalization of the flavin cofactor.
Authors: Saleem-Batcha, R. / Stull, F. / Sanders, J.N. / Moore, B.S. / Palfey, B.A. / Houk, K.N. / Teufel, R.
History
DepositionFeb 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative FAD-dependent oxygenase EncM
B: Putative FAD-dependent oxygenase EncM
C: Putative FAD-dependent oxygenase EncM
D: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,69616
Polymers200,2974
Non-polymers3,39812
Water33,3281850
1
A: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9244
Polymers50,0741
Non-polymers8503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9244
Polymers50,0741
Non-polymers8503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9244
Polymers50,0741
Non-polymers8503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9244
Polymers50,0741
Non-polymers8503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.824, 175.153, 131.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11B-959-

HOH

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Components

#1: Protein
Putative FAD-dependent oxygenase EncM


Mass: 50074.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces maritimus (bacteria) / Gene: encM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KHK2
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1850 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.1M HEPES-Na (pH 7.5), 0.2M calcium acetate, 20% PEG 3350, VAPOR DIFFUSION, Sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.386→48.484 Å / Num. obs: 359223 / % possible obs: 94.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.1381001681 Å2 / Net I/σ(I): 12.3
Reflection shellResolution: 1.39→48.48 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11rc1_2513: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XLO

4xlo


Resolution: 1.386→48.484 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 17904 4.99 %
Rwork0.1922 --
obs0.1932 358921 94.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.386→48.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13920 0 228 1850 15998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114534
X-RAY DIFFRACTIONf_angle_d1.22719839
X-RAY DIFFRACTIONf_dihedral_angle_d18.5775119
X-RAY DIFFRACTIONf_chiral_restr0.1142155
X-RAY DIFFRACTIONf_plane_restr0.0092579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3858-1.40150.31032060.30133951X-RAY DIFFRACTION33
1.4015-1.4180.31544610.29658478X-RAY DIFFRACTION71
1.418-1.43530.32485470.293510137X-RAY DIFFRACTION85
1.4353-1.45350.29485730.285210554X-RAY DIFFRACTION89
1.4535-1.47260.30865840.271611080X-RAY DIFFRACTION92
1.4726-1.49280.27875900.264411412X-RAY DIFFRACTION95
1.4928-1.51410.28496460.254611700X-RAY DIFFRACTION98
1.5141-1.53670.2745990.245512015X-RAY DIFFRACTION100
1.5367-1.56070.26836170.237611863X-RAY DIFFRACTION100
1.5607-1.58630.27356370.23211890X-RAY DIFFRACTION100
1.5863-1.61370.23886500.225411936X-RAY DIFFRACTION100
1.6137-1.6430.26246390.223911986X-RAY DIFFRACTION100
1.643-1.67460.25866190.222711917X-RAY DIFFRACTION100
1.6746-1.70880.25416000.222911985X-RAY DIFFRACTION99
1.7088-1.7460.2395990.219411876X-RAY DIFFRACTION99
1.746-1.78660.24466140.214511991X-RAY DIFFRACTION100
1.7866-1.83130.24676010.215911949X-RAY DIFFRACTION100
1.8313-1.88080.21896170.210212026X-RAY DIFFRACTION100
1.8808-1.93610.24126410.209511964X-RAY DIFFRACTION100
1.9361-1.99860.22796500.208611913X-RAY DIFFRACTION99
1.9986-2.070.22546650.206811868X-RAY DIFFRACTION99
2.07-2.15290.21396550.196111937X-RAY DIFFRACTION99
2.1529-2.25090.22836620.187611904X-RAY DIFFRACTION99
2.2509-2.36960.20866130.191711950X-RAY DIFFRACTION99
2.3696-2.5180.20646590.186411748X-RAY DIFFRACTION98
2.518-2.71240.2135180.190511854X-RAY DIFFRACTION97
2.7124-2.98540.20476140.183511829X-RAY DIFFRACTION97
2.9854-3.41730.19236210.176311729X-RAY DIFFRACTION96
3.4173-4.3050.16985770.156611690X-RAY DIFFRACTION95
4.305-48.51380.17176300.164211885X-RAY DIFFRACTION95

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