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- PDB-6jhm: Crystal structure of Flavin-dependent Monooxygenase HadA -

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Basic information

Entry
Database: PDB / ID: 6jhm
TitleCrystal structure of Flavin-dependent Monooxygenase HadA
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
4-hydroxybutyryl-coa dehydratase, domain 1 / 4-hydroxybutyryl-coa dehydratase, domain 1 / 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 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 ...4-hydroxybutyryl-coa dehydratase, domain 1 / 4-hydroxybutyryl-coa dehydratase, domain 1 / 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 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / 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
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
AuthorsJaruwat, A. / Pimviriyakul, P. / Chitnumsub, P. / Chaiyen, P.
CitationJournal: Chembiochem / Year: 2019
Title: Identification of a Hotspot Residue for Improving the Thermostability of a Flavin-Dependent Monooxygenase.
Authors: Pongpamorn, P. / Watthaisong, P. / Pimviriyakul, P. / Jaruwat, A. / Lawan, N. / Chitnumsub, P. / Chaiyen, P.
History
DepositionFeb 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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: Chlorophenol monooxygenase
B: Chlorophenol monooxygenase
C: Chlorophenol monooxygenase
D: Chlorophenol monooxygenase


Theoretical massNumber of molelcules
Total (without water)234,4934
Polymers234,4934
Non-polymers00
Water15,673870
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20470 Å2
ΔGint-152 kcal/mol
Surface area63220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.924, 128.143, 182.182
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
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) / Strain (production host): BL21(DE3)
References: UniProt: Q53008, 4-hydroxyphenylacetate 3-monooxygenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 870 / 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: 2.44 Å3/Da / Density % sol: 49.53 % / 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: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→20.79 Å / Num. obs: 102154 / % possible obs: 99.8 % / Redundancy: 11 % / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.038 / Rrim(I) all: 0.131 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.3470.50850240.9350.2060.54999.9
12.6-20.689.60.0535160.9920.0170.05672.8

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Processing

Software
NameVersionClassification
Aimless0.6.3data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G5E

4g5e


Resolution: 2.3→20.69 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.886 / SU B: 7.722 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.251
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 5068 5 %RANDOM
Rwork0.1998 ---
obs0.2028 96975 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 120 Å2 / Biso mean: 23.457 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å2-0 Å2-0 Å2
2---0.82 Å20 Å2
3---1.77 Å2
Refinement stepCycle: final / Resolution: 2.3→20.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15539 0 0 870 16409
Biso mean---24.18 -
Num. residues----1941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01515940
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713966
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.73821604
X-RAY DIFFRACTIONr_angle_other_deg0.5181.69932687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74251930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.50918.56722
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.165152244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.89315136
X-RAY DIFFRACTIONr_chiral_restr0.070.21986
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023096
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 347 -
Rwork0.256 7013 -
all-7360 -
obs--99.99 %

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