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- PDB-4kcf: X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2... -

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Basic information

Entry
Database: PDB / ID: 4kcf
TitleX-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose
ComponentsFAD-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / KijD3 / fatty acyl-CoA dehydrogenase family / kijanose / kijanimicin / FAD / Flavoprotein / class D flavin containing monooxygenases / N-oxygenase / nucleotide linked sugar / dTDP-3-amino-2 / 3 / 6-trideoxy-4-keto-3-methyl-D-glucose / FMN
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain ...Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-AKM / FLAVIN MONONUCLEOTIDE / FAD-dependent oxidoreductase
Similarity search - Component
Biological speciesActinomadura kijaniata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsHolden, H.M. / Thoden, J.B. / Branch, M.C. / Zimmer, A.L. / Bruender, N.A.
CitationJournal: Biochemistry / Year: 2013
Title: Active site architecture of a sugar N-oxygenase.
Authors: Thoden, J.B. / Branch, M.C. / Zimmer, A.L. / Bruender, N.A. / Holden, H.M.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Atomic model / Non-polymer description
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3453
Polymers48,3271
Non-polymers1,0182
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: FAD-dependent oxidoreductase
hetero molecules

A: FAD-dependent oxidoreductase
hetero molecules

A: FAD-dependent oxidoreductase
hetero molecules

A: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,38112
Polymers193,3104
Non-polymers4,0718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area15460 Å2
ΔGint-99 kcal/mol
Surface area53290 Å2
MethodPISA
3
A: FAD-dependent oxidoreductase
hetero molecules

A: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6906
Polymers96,6552
Non-polymers2,0354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area4500 Å2
ΔGint-25 kcal/mol
Surface area29880 Å2
MethodPISA
4
A: FAD-dependent oxidoreductase
hetero molecules

A: FAD-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6906
Polymers96,6552
Non-polymers2,0354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4430 Å2
ΔGint-25 kcal/mol
Surface area29950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.828, 81.297, 152.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein FAD-dependent oxidoreductase


Mass: 48327.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura kijaniata (bacteria) / Gene: KijD3 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: B3TMR1
#2: Chemical ChemComp-AKM / [(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate / dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose (hydrated at C4)


Mass: 561.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H29N3O14P2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% pentaerythritol propoxylate 5/4 100 mM MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2012
RadiationMonochromator: double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.098→76.31 Å / Num. all: 23596 / Num. obs: 23596 / % possible obs: 90.4 % / Redundancy: 5.7 % / Rsym value: 0.069
Reflection shellResolution: 2.098→2.18 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 17.5 / Num. unique all: 2209 / Rsym value: 0.11 / % possible all: 85.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M9V

3m9v


Resolution: 2.098→76.31 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.307 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22518 1193 5.1 %RANDOM
Rwork0.17492 ---
obs0.17742 23596 89.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.777 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å20 Å20 Å2
2---0.93 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.098→76.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 61 102 3188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213157
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2691.994315
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.00122.093129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19515472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9781535
X-RAY DIFFRACTIONr_chiral_restr0.1310.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2181.52023
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07823226
X-RAY DIFFRACTIONr_scbond_it3.12431134
X-RAY DIFFRACTIONr_scangle_it4.8394.51089
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.098→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 67 -
Rwork0.18 1465 -
obs--79.58 %

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