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- PDB-6fyg: The crystal structure of EncM V135T mutant -

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Basic information

Entry
Database: PDB / ID: 6fyg
TitleThe crystal structure of EncM V135T mutant
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 / Putative FAD-dependent oxygenase EncM
Similarity search - Component
Biological speciesStreptomyces maritimus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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
C: Putative FAD-dependent oxygenase EncM
D: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,4488
Polymers200,3054
Non-polymers3,1424
Water7,422412
1
A: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8622
Polymers50,0761
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8622
Polymers50,0761
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8622
Polymers50,0761
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8622
Polymers50,0761
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.806, 174.229, 131.773
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: 50076.344 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 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
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: 2.55→48.69 Å / Num. obs: 61948 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 18.1
Reflection shellResolution: 2.55→2.69 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: 2.55→48.686 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.36
RfactorNum. reflection% reflection
Rfree0.246 2988 4.83 %
Rwork0.2007 --
obs0.2029 61887 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→48.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14004 0 212 412 14628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514600
X-RAY DIFFRACTIONf_angle_d0.79519940
X-RAY DIFFRACTIONf_dihedral_angle_d17.3685140
X-RAY DIFFRACTIONf_chiral_restr0.052160
X-RAY DIFFRACTIONf_plane_restr0.0062596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.59180.35091380.26132754X-RAY DIFFRACTION100
2.5918-2.63650.34211530.24782769X-RAY DIFFRACTION100
2.6365-2.68450.3311530.23742745X-RAY DIFFRACTION100
2.6845-2.73610.31341450.23542830X-RAY DIFFRACTION100
2.7361-2.79190.26641320.22372771X-RAY DIFFRACTION100
2.7919-2.85260.31471610.2132740X-RAY DIFFRACTION100
2.8526-2.9190.25771290.21832800X-RAY DIFFRACTION100
2.919-2.9920.29181330.22372800X-RAY DIFFRACTION100
2.992-3.07290.31441380.2292796X-RAY DIFFRACTION100
3.0729-3.16330.27161590.22722764X-RAY DIFFRACTION100
3.1633-3.26530.24211440.21752775X-RAY DIFFRACTION100
3.2653-3.3820.25071540.20612786X-RAY DIFFRACTION100
3.382-3.51740.27211440.21042805X-RAY DIFFRACTION100
3.5174-3.67740.2371280.19432799X-RAY DIFFRACTION100
3.6774-3.87120.2241380.18932835X-RAY DIFFRACTION100
3.8712-4.11370.19761410.17732801X-RAY DIFFRACTION100
4.1137-4.43110.22781290.17222844X-RAY DIFFRACTION100
4.4311-4.87660.18291690.14992787X-RAY DIFFRACTION100
4.8766-5.58140.18081230.17252877X-RAY DIFFRACTION100
5.5814-7.02860.23111390.20512878X-RAY DIFFRACTION100
7.0286-48.69440.19751380.19312943X-RAY DIFFRACTION98

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