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- PDB-7e8p: Crystal structure of a Flavin-dependent Monooxygenase HadA wild t... -

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Basic information

Entry
Database: PDB / ID: 7e8p
TitleCrystal structure of a Flavin-dependent Monooxygenase HadA wild type complexed with reduced FAD and 4-nitrophenol
ComponentsChlorophenol monooxygenase
KeywordsOXIDOREDUCTASE / flavin monooxygenase / chlorophenol 4-monooxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors / monooxygenase activity
Similarity search - Function
HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / 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 ...HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / 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 / Mainly Alpha
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / P-NITROPHENOL / Chlorophenol monooxygenase
Similarity search - Component
Biological speciesRalstonia pickettii DTP0602 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Model detailsCrystal structure of Flavin-dependent Monooxygenase HadA with FADH2 and 4-nitophenol
AuthorsPimviriyakul, P. / Jaruwat, A. / Chitnumsub, P. / Chaiyen, P.
Funding support Thailand, 2items
OrganizationGrant numberCountry
The Thailand Research Fund (TRF)MRG6280185 Thailand
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural insights into a flavin-dependent dehalogenase HadA explain catalysis and substrate inhibition via quadruple pi-stacking.
Authors: Pimviriyakul, P. / Jaruwat, A. / Chitnumsub, P. / Chaiyen, P.
History
DepositionMar 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chlorophenol monooxygenase
B: Chlorophenol monooxygenase
C: Chlorophenol monooxygenase
D: Chlorophenol monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,06011
Polymers234,4934
Non-polymers3,5687
Water15,817878
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31510 Å2
ΔGint-195 kcal/mol
Surface area59610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.817, 161.855, 168.647
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chlorophenol monooxygenase / Chlorophenol-4-hydroxylase / chlorophenol 4-monooxygenase


Mass: 58623.164 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii DTP0602 (bacteria) / Gene: hadA / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q53008, 4-hydroxyphenylacetate 3-monooxygenase
#2: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 878 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.79 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5
Details: 0.1 M Bis-Tris propane pH 6.5, 0.35 M sodium citrate tribasic dihydrate and 24% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Mar 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→20.74 Å / Num. obs: 118305 / % possible obs: 99.3 % / Redundancy: 5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.052 / Rrim(I) all: 0.122 / Net I/σ(I): 9.9 / Num. measured all: 586952
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.343.30.4261912157430.8790.2640.5052.498.1
12.6-20.747.30.0540905600.9990.0180.05324.669

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JHM

6jhm


Resolution: 2.3→20.71 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.871 / SU B: 8.258 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 5826 5 %RANDOM
Rwork0.2109 ---
obs0.2137 110286 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 124.52 Å2 / Biso mean: 20.662 Å2 / Biso min: 2.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å2-0 Å20 Å2
2--2.05 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 2.3→20.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15450 0 242 878 16570
Biso mean--18.88 22.31 -
Num. residues----1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01316120
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714496
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.65221900
X-RAY DIFFRACTIONr_angle_other_deg1.2891.59133508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05451920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04521.39971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53152584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.14415140
X-RAY DIFFRACTIONr_chiral_restr0.3060.22008
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023660
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 388 -
Rwork0.291 7585 -
all-7973 -
obs--92.34 %

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