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- PDB-4xlo: Crystal Structure of EncM (crystallized with 4 mM NADPH) -

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Basic information

Entry
Database: PDB / ID: 4xlo
TitleCrystal Structure of EncM (crystallized with 4 mM NADPH)
ComponentsFAD-dependent oxygenase EncM
KeywordsOXIDOREDUCTASE / Flavoenzyme / NADPH / vanillyl-alcohol oxidase/p-cresol methylhydroxylase fold / oxygenase
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 / Putative FAD-dependent oxygenase EncM
Similarity search - Component
Biological speciesStreptomyces maritimus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsTeufel, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI47818 United States
Citation
Journal: Nature / Year: 2013
Title: Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement.
Authors: Teufel, R. / Miyanaga, A. / Michaudel, Q. / Stull, F. / Louie, G. / Noel, J.P. / Baran, P.S. / Palfey, B. / Moore, B.S.
#1: Journal: Nature / Year: 2013
Title: Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement
Authors: Teufel, R. / Miyanaga, A. / Michaudel, Q. / Stull, F. / Louie, G. / Noel, J.P. / Baran, P.S. / Palfey, B. / Moore, B.S.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)203,4408
Polymers200,2974
Non-polymers3,1424
Water38,1922120
1
A: FAD-dependent oxygenase EncM
C: FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7204
Polymers100,1492
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-37 kcal/mol
Surface area30040 Å2
MethodPISA
2
B: FAD-dependent oxygenase EncM
D: FAD-dependent oxygenase EncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7204
Polymers100,1492
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-37 kcal/mol
Surface area30210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.060, 175.020, 132.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11D-1090-

HOH

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Components

#1: Protein
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: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2120 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 5 mg/mL EncM in 4 mM NADPH, 5 mM TES sodium, pH 7.7, 10% v/v glycerol, reservoir: 0.1 M HEPES sodium, pH 7.5, 0.2 M calcium acetate, 20% w/v PEG3350
PH range: 7.5-7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→29.69 Å / Num. obs: 219275 / % possible obs: 98.35 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 28.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BVG

2bvg


Resolution: 1.67→29.69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.669 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 12765 5.9 %RANDOM
Rwork0.1847 204554 --
obs0.1874 204554 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.84 Å2 / Biso mean: 23.32 Å2 / Biso min: 8.45 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.67→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14001 0 212 2120 16333
Biso mean--12.89 38.05 -
Num. residues----1841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01914749
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.97220173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72551873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46222.559637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.389152147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.53515129
X-RAY DIFFRACTIONr_chiral_restr0.1590.22180
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02111549
LS refinement shellResolution: 1.671→1.714 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 807 -
Rwork0.417 12480 -
all-13287 -
obs--84.39 %

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