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

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Basic information

Entry
Database: PDB / ID: 2yyi
TitleCrystal structure of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase complexed with FAD
Components4-hydroxyphenylacetate-3-hydroxylase
KeywordsOXIDOREDUCTASE / Structurome / RIKEN SPring-8 Center / oxygnase component / 4-hydroxyphenylacetate 3-monooxygenase / two-component flavin diffusible monooxygenase / FAD complex
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
FLAVIN-ADENINE DINUCLEOTIDE / 4-hydroxyphenylacetate 3-monooxygenase oxygenase component
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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)55,5396
Polymers54,3691
Non-polymers1,1705
Water9,224512
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)222,15524
Polymers217,4764
Non-polymers4,67920
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 area35410 Å2
ΔGint-449 kcal/mol
Surface area56210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.786, 98.370, 130.022
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-1501-

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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
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: Dec 10, 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: 1.66→41.04 Å / Num. all: 67442 / Num. obs: 67442 / Redundancy: 3.7 % / Biso Wilson estimate: 18.605 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 25
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.163 / Num. unique all: 6605

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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: 1.66→41.04 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.182 3398 -RANDOM
Rwork0.169 ---
all-68877 --
obs-67442 96.4 %-
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20 Å2
2--4.95 Å20 Å2
3----2.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-30 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.66→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 73 512 4363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d1.83
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 (%)
1.66-1.760.22215380.20581098195.1
1.76-1.90.20835740.18081110794.8
1.9-2.090.18545660.16531121695
2.09-2.390.17625530.16511131995.1
2.39-3.020.17825740.16711140395
3.02-41.040.17495930.16521141694.8

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