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- PDB-6fyc: The crystal structure of EncM L144M mutant complex with dioxygen ... -

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Basic information

Entry
Database: PDB / ID: 6fyc
TitleThe crystal structure of EncM L144M mutant complex with dioxygen under 15 bars O2 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 / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Berberine/berberine-like / Berberine and berberine like / 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 / Oxygen oxidoreductase covalent FAD-binding site / Oxygen oxidoreductases covalent FAD-binding site. / Berberine/berberine-like / Berberine and berberine like / 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: 2 Å
AuthorsSaleem-Batcha, R. / Teufel, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationTE931/2-1 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
DepositionMar 11, 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8206
Polymers100,1852
Non-polymers1,6354
Water3,603200
1
A: Putative FAD-dependent oxygenase EncM
hetero molecules

B: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8206
Polymers100,1852
Non-polymers1,6354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544-x+1/2,-y-1,z-1/21
Buried area6640 Å2
ΔGint-28 kcal/mol
Surface area30370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.794, 87.358, 128.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Putative FAD-dependent oxygenase EncM


Mass: 50092.410 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES-Na, 0.2M Calcium Acetate, 20% - 30% PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2→43.68 Å / Num. obs: 61351 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.4
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.54

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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: 2→43.679 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.54
RfactorNum. reflection% reflection
Rfree0.2722 3059 5 %
Rwork0.2399 --
obs0.2415 61223 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→43.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6900 0 110 200 7210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097242
X-RAY DIFFRACTIONf_angle_d1.1139884
X-RAY DIFFRACTIONf_dihedral_angle_d19.7822556
X-RAY DIFFRACTIONf_chiral_restr0.0631068
X-RAY DIFFRACTIONf_plane_restr0.0081286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03130.29961530.27072600X-RAY DIFFRACTION100
2.0313-2.06460.36911390.27412599X-RAY DIFFRACTION100
2.0646-2.10020.31231500.27482633X-RAY DIFFRACTION100
2.1002-2.13830.33871190.26422610X-RAY DIFFRACTION100
2.1383-2.17950.30961530.25152605X-RAY DIFFRACTION100
2.1795-2.2240.28321330.25812608X-RAY DIFFRACTION100
2.224-2.27230.34271410.24742605X-RAY DIFFRACTION100
2.2723-2.32520.29131310.24632638X-RAY DIFFRACTION100
2.3252-2.38330.30011420.24292598X-RAY DIFFRACTION100
2.3833-2.44770.28541420.2452621X-RAY DIFFRACTION100
2.4477-2.51980.30431330.24572633X-RAY DIFFRACTION100
2.5198-2.60110.34991310.25412626X-RAY DIFFRACTION100
2.6011-2.6940.27951190.24932653X-RAY DIFFRACTION100
2.694-2.80190.2821430.24492634X-RAY DIFFRACTION100
2.8019-2.92940.28961420.25042647X-RAY DIFFRACTION100
2.9294-3.08380.29251410.24872635X-RAY DIFFRACTION100
3.0838-3.27690.26141480.25082650X-RAY DIFFRACTION100
3.2769-3.52980.27611350.24462665X-RAY DIFFRACTION100
3.5298-3.88490.26091450.23152667X-RAY DIFFRACTION100
3.8849-4.44650.22461300.22082715X-RAY DIFFRACTION100
4.4465-5.60030.24731450.21882716X-RAY DIFFRACTION100
5.6003-43.68940.25851440.23982806X-RAY DIFFRACTION98

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