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- PDB-6fow: The crystal structure of EncM complexed with dioxygen under 10 ba... -

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Basic information

Entry
Database: PDB / ID: 6fow
TitleThe crystal structure of EncM complexed with dioxygen under 10 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 / 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: 2.04 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 1.2Feb 15, 2023Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Feb 22, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.4Feb 7, 2024Group: 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

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)203,56812
Polymers200,2974
Non-polymers3,2708
Water12,574698
1
A: Putative FAD-dependent oxygenase EncM
B: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7846
Polymers100,1492
Non-polymers1,6354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-34 kcal/mol
Surface area30020 Å2
MethodPISA
2
C: Putative FAD-dependent oxygenase EncM
D: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7846
Polymers100,1492
Non-polymers1,6354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-30 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.210, 174.852, 132.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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.: 4 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.1M HEPES-Na, 0.2M calcium acetate, 20% PEG 3350, pH 7.5

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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: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→49.04 Å / Num. obs: 117300 / % possible obs: 96.4 % / Redundancy: 3.5 % / Net I/σ(I): 7.1
Reflection shellResolution: 2.03→49.04 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: 2.04→43.713 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.77
RfactorNum. reflection% reflection
Rfree0.229 5886 5.03 %
Rwork0.1917 --
obs0.1936 117121 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.04→43.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13920 0 220 698 14838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514640
X-RAY DIFFRACTIONf_angle_d0.75520012
X-RAY DIFFRACTIONf_dihedral_angle_d18.9985164
X-RAY DIFFRACTIONf_chiral_restr0.052168
X-RAY DIFFRACTIONf_plane_restr0.0052616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0398-2.0630.37451640.34393054X-RAY DIFFRACTION80
2.063-2.08730.41722090.33493814X-RAY DIFFRACTION100
2.0873-2.11270.41741920.33773774X-RAY DIFFRACTION99
2.1127-2.13950.39511840.31243791X-RAY DIFFRACTION99
2.1395-2.16760.34911910.28433799X-RAY DIFFRACTION99
2.1676-2.19730.35972030.26993785X-RAY DIFFRACTION99
2.1973-2.22870.30242140.24673733X-RAY DIFFRACTION98
2.2287-2.2620.27971790.23223807X-RAY DIFFRACTION98
2.262-2.29730.27892020.22833715X-RAY DIFFRACTION97
2.2973-2.3350.28792270.22393724X-RAY DIFFRACTION98
2.335-2.37520.27751960.21783729X-RAY DIFFRACTION98
2.3752-2.41840.26982130.21213792X-RAY DIFFRACTION98
2.4184-2.46490.27011900.20883725X-RAY DIFFRACTION97
2.4649-2.51520.23152090.20493681X-RAY DIFFRACTION96
2.5152-2.56990.23821740.20563526X-RAY DIFFRACTION91
2.5699-2.62970.25391770.21073548X-RAY DIFFRACTION93
2.6297-2.69540.21791780.18763808X-RAY DIFFRACTION98
2.6954-2.76830.25432070.19123768X-RAY DIFFRACTION98
2.7683-2.84980.25822060.18833780X-RAY DIFFRACTION98
2.8498-2.94170.22951880.1873815X-RAY DIFFRACTION98
2.9417-3.04680.21791760.17943764X-RAY DIFFRACTION98
3.0468-3.16880.20881880.18013801X-RAY DIFFRACTION98
3.1688-3.3130.21112000.18043755X-RAY DIFFRACTION97
3.313-3.48760.2212350.18323699X-RAY DIFFRACTION97
3.4876-3.7060.17832210.16783588X-RAY DIFFRACTION93
3.706-3.99190.20141930.15143522X-RAY DIFFRACTION90
3.9919-4.39330.15592100.14423768X-RAY DIFFRACTION97
4.3933-5.02820.16761980.13593782X-RAY DIFFRACTION96
5.0282-6.3320.20831910.18773772X-RAY DIFFRACTION95
6.332-43.7230.22141710.19883616X-RAY DIFFRACTION88

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