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- PDB-2yyg: Crystal structure of the oxygenase component (HpaB) of 4-hydroxyp... -

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Basic information

Entry
Database: PDB / ID: 2yyg
TitleCrystal structure of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase
Components4-hydroxyphenylacetate-3-hydroxylase
KeywordsOXIDOREDUCTASE / Structurome / RIKEN SPring-8 Center / oxygnase component / 4-hydroxyphenylacetate 3-monooxygenase / two-component flavin diffusible monooxygenase
Function / homology
Function and homology information


4-hydroxyphenylacetate 3-monooxygenase activity / 4-hydroxyphenylacetate 3-monooxygenase / oxidoreductase activity, acting on the CH-CH group of donors / phenylacetate catabolic process / flavin adenine dinucleotide binding
Similarity search - Function
4-HPA 3-monooxygenase large component, Deinococcus-type / 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 / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 ...4-HPA 3-monooxygenase large component, Deinococcus-type / 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 / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / 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
4-hydroxyphenylacetate 3-monooxygenase oxygenase component
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, S.-H. / Hisano, T. / Takeda, K. / Iwasaki, W. / Ebihara, A. / Miki, K.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of the Oxygenase Component (HpaB) of the 4-Hydroxyphenylacetate 3-Monooxygenase from Thermus thermophilus HB8
Authors: Kim, S.-H. / Hisano, T. / Takeda, K. / Iwasaki, W. / Ebihara, A. / Miki, K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and preliminary X-ray analysis of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8
Authors: Kim, S.-H. / Miyatake, H. / Hisano, T. / Iwasaki, W. / Ebihara, A. / Miki, K.
History
DepositionApr 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: 4-hydroxyphenylacetate-3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8496
Polymers54,3691
Non-polymers4805
Water6,431357
1
A: 4-hydroxyphenylacetate-3-hydroxylase
hetero molecules

A: 4-hydroxyphenylacetate-3-hydroxylase
hetero molecules

A: 4-hydroxyphenylacetate-3-hydroxylase
hetero molecules

A: 4-hydroxyphenylacetate-3-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,39724
Polymers217,4764
Non-polymers1,92120
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 area29390 Å2
ΔGint-475 kcal/mol
Surface area58860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.377, 99.214, 131.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1329-

HOH

21A-1348-

HOH

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Components

#1: Protein 4-hydroxyphenylacetate-3-hydroxylase / 4-hydroxyphenylacetate 3-monooxygenase


Mass: 54369.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJP8, EC: 1.14.13.3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5M ammonium sulfate, 0.1M Tris-HCl, 25% (v/v) glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 21, 2005 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→47.01 Å / Num. all: 38621 / Num. obs: 38621 / Redundancy: 4.3 % / Biso Wilson estimate: 25.304 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.165 / Num. unique all: 3220

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Processing

Software
NameVersionClassification
HKL-2000data collection
ARP/wARPmodel building
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YYK

2yyk


Resolution: 2→47.01 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1950 -RANDOM
Rwork0.18 ---
all-40711 --
obs-38617 83.1 %-
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--9.19 Å20 Å20 Å2
2--19.01 Å20 Å2
3----9.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-30 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 25 357 4116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
2-2.130.26712810.242556394.9
2.13-2.290.24293170.2202630895
2.29-2.520.2363010.1905644095.5
2.52-2.880.22783290.1917661295
2.88-3.630.19283630.1704674694.6
3.63-47.010.1743590.1603694094.8

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