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- PDB-3k87: Crystal structure of NADH:FAD oxidoreductase (TftC) - FAD complex -

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Basic information

Entry
Database: PDB / ID: 3k87
TitleCrystal structure of NADH:FAD oxidoreductase (TftC) - FAD complex
ComponentsChlorophenol-4-monooxygenase component 1
KeywordsOXIDOREDUCTASE / NADH:FAD oxidoreductase / Monooxygenase
Function / homology
Function and homology information


FAD reductase (NADH) / oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / pyrimidine nucleobase catabolic process / riboflavin reductase (NADPH) activity / monooxygenase activity / FMN binding / protein homodimerization activity
Similarity search - Function
: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADH:FAD oxidoreductase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKang, C.H. / Webb, B.N.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:FAD oxidoreductase (TftC) of Burkholderia cepacia AC1100.
Authors: Webb, B.N. / Ballinger, J.W. / Kim, E. / Belchik, S.M. / Lam, K.S. / Youn, B. / Nissen, M.S. / Xun, L. / Kang, C.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Chlorophenol-4-monooxygenase component 1
B: Chlorophenol-4-monooxygenase component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3224
Polymers39,7512
Non-polymers1,5712
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-47.9 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.529, 111.529, 102.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Chlorophenol-4-monooxygenase component 1


Mass: 19875.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Strain: AC1100 / Gene: tftC / Plasmid: pET30 LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O87008
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Potassium formate, 20% w/v PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: Pt-coated Si
RadiationMonochromator: KOHZU: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→35.15 Å / Num. obs: 35354

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3K86

3k86


Resolution: 2→18.875 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 1251 4.87 %
Rwork0.161 --
obs0.163 25673 79.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.486 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 114.11 Å2 / Biso mean: 31.055 Å2 / Biso min: 5.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.691 Å2-0 Å20 Å2
2---0.691 Å20 Å2
3---1.382 Å2
Refinement stepCycle: LAST / Resolution: 2→18.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 106 378 2926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162608
X-RAY DIFFRACTIONf_angle_d1.7373575
X-RAY DIFFRACTIONf_chiral_restr0.127404
X-RAY DIFFRACTIONf_plane_restr0.012443
X-RAY DIFFRACTIONf_dihedral_angle_d21.947933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.080.2951280.2522479260772
2.08-2.1740.311310.2322602273377
2.174-2.2890.2821410.2072684282579
2.289-2.4320.2911450.1952692283780
2.432-2.6190.251350.1782795293082
2.619-2.8820.1951400.1552792293282
2.882-3.2970.1871450.1372850299584
3.297-4.1470.181470.1262833298084
4.147-18.8750.1621390.1382695283479

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