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- PDB-3k88: Crystal structure of NADH:FAD oxidoreductase (TftC) - FAD, NADH c... -

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Basic information

Entry
Database: PDB / ID: 3k88
TitleCrystal structure of NADH:FAD oxidoreductase (TftC) - FAD, NADH 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH:FAD oxidoreductase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKang, C. / 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)42,6496
Polymers39,7512
Non-polymers2,8984
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-42.8 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.094, 113.094, 101.682
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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
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: 1.58→35.27 Å / Num. obs: 35903

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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→19.236 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 1347 4.93 %
Rwork0.164 --
obs0.166 27350 83.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.963 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 111.53 Å2 / Biso mean: 31.772 Å2 / Biso min: 14.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.207 Å20 Å20 Å2
2--0.207 Å20 Å2
3---2.787 Å2
Refinement stepCycle: LAST / Resolution: 2→19.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 194 257 2897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222708
X-RAY DIFFRACTIONf_angle_d2.5043728
X-RAY DIFFRACTIONf_chiral_restr0.146404
X-RAY DIFFRACTIONf_plane_restr0.017452
X-RAY DIFFRACTIONf_dihedral_angle_d22.2581024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0720.3041150.2542139225470
2.072-2.1540.2711330.222551268481
2.154-2.2520.2381360.1972597273384
2.252-2.3710.2761310.1932695282685
2.371-2.5190.2381410.1782633277486
2.519-2.7130.2081390.1592716285587
2.713-2.9850.2091380.1542698283687
2.985-3.4150.1841380.1462687282587
3.415-4.2950.1681410.142702284386
4.295-19.2360.1691350.1512585272083

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