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- PDB-6fp3: The crystal structure of EncM complexed with dioxygen under 5 bar... -

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Basic information

Entry
Database: PDB / ID: 6fp3
TitleThe crystal structure of EncM complexed with dioxygen under 5 bar of oxygen pressure.
ComponentsPutative FAD-dependent oxygenase EncM
KeywordsFLAVOPROTEIN / nooxygenase / 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 / Berberine/berberine-like / Berberine and berberine like / 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 ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / 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 / Resolution: 1.976 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 9, 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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
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
Water18,3391018
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 area7110 Å2
ΔGint-34 kcal/mol
Surface area29830 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-37 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.690, 175.144, 131.760
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

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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 / 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 / Oxygen


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


Mass: 18.015 Da / Num. of mol.: 1018 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
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: 1.975→48.91 Å / Num. obs: 131502 / % possible obs: 98.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.1701402375 Å2 / Net I/σ(I): 7.3
Reflection shellHighest resolution: 1.975 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11rc1_2513: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.976→48.91 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 6560 5 %
Rwork0.1819 --
obs0.1834 131257 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.976→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13920 0 220 1018 15158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614640
X-RAY DIFFRACTIONf_angle_d0.86320012
X-RAY DIFFRACTIONf_dihedral_angle_d18.85164
X-RAY DIFFRACTIONf_chiral_restr0.0532168
X-RAY DIFFRACTIONf_plane_restr0.0062616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9759-1.99840.3161790.27043154X-RAY DIFFRACTION76
1.9984-2.02190.29451910.24174168X-RAY DIFFRACTION99
2.0219-2.04650.29182210.22774190X-RAY DIFFRACTION99
2.0465-2.07240.27212270.22984133X-RAY DIFFRACTION99
2.0724-2.09970.31382020.23854165X-RAY DIFFRACTION99
2.0997-2.12850.28352220.22484153X-RAY DIFFRACTION99
2.1285-2.15890.25592170.2044173X-RAY DIFFRACTION99
2.1589-2.19110.24182320.20764170X-RAY DIFFRACTION99
2.1911-2.22530.2461910.20434171X-RAY DIFFRACTION99
2.2253-2.26180.2582230.2034075X-RAY DIFFRACTION97
2.2618-2.30080.22312290.20074117X-RAY DIFFRACTION98
2.3008-2.34270.23352140.19554157X-RAY DIFFRACTION100
2.3427-2.38770.2462060.20034215X-RAY DIFFRACTION100
2.3877-2.43650.23822210.19294225X-RAY DIFFRACTION100
2.4365-2.48940.232320.19024168X-RAY DIFFRACTION100
2.4894-2.54730.22912650.18764159X-RAY DIFFRACTION100
2.5473-2.6110.23012450.19514165X-RAY DIFFRACTION100
2.611-2.68160.21642350.19234209X-RAY DIFFRACTION100
2.6816-2.76050.2412250.19324168X-RAY DIFFRACTION100
2.7605-2.84960.22512210.1864213X-RAY DIFFRACTION100
2.8496-2.95150.21712450.18554183X-RAY DIFFRACTION100
2.9515-3.06960.2112110.18554242X-RAY DIFFRACTION100
3.0696-3.20930.21672210.18134189X-RAY DIFFRACTION99
3.2093-3.37850.22651840.18174112X-RAY DIFFRACTION96
3.3785-3.59010.20811930.17164268X-RAY DIFFRACTION100
3.5901-3.86720.18292140.1534263X-RAY DIFFRACTION100
3.8672-4.25610.13432260.154261X-RAY DIFFRACTION100
4.2561-4.87150.15711990.14214294X-RAY DIFFRACTION100
4.8715-6.13570.20782460.17664265X-RAY DIFFRACTION99
6.1357-48.92470.20712230.194272X-RAY DIFFRACTION95

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