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- PDB-2ecu: Crystal structure of flavin reductase component (HpaC) of 4-hydro... -

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Basic information

Entry
Database: PDB / ID: 2ecu
TitleCrystal structure of flavin reductase component (HpaC) of 4-hydroxyphenylacetate 3-monooxygenase
Componentsflavin reductase (HpaC) of 4-hydroxyphenylacetate 3-monooxygnease
KeywordsOXIDOREDUCTASE / flavin reductase / flavin diffusible / two-component monooxygenase
Function / homology
Function and homology information


flavin reductase (NADH) / pyrimidine nucleobase catabolic process / flavin reductase (NADH) activity / riboflavin reductase (NADPH) activity / FMN binding
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
Chem-1PG / 4-hydroxyphenylacetate 3-monooxygenase, reductase component
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKim, S.H. / Hisano, T. / Iwasaki, W. / Ebihara, A. / Miki, K.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of the flavin reductase component (HpaC) of 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8: Structural basis for the flavin affinity
Authors: Kim, S.H. / Hisano, T. / Iwasaki, W. / Ebihara, A. / Miki, K.
History
DepositionFeb 14, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Apr 3, 2024Group: 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: flavin reductase (HpaC) of 4-hydroxyphenylacetate 3-monooxygnease
B: flavin reductase (HpaC) of 4-hydroxyphenylacetate 3-monooxygnease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9184
Polymers32,1192
Non-polymers7992
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-47 kcal/mol
Surface area13040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.587, 43.690, 74.715
Angle α, β, γ (deg.)90.00, 92.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein flavin reductase (HpaC) of 4-hydroxyphenylacetate 3-monooxygnease / Hypothetical protein TTHA0961


Mass: 16059.578 Da / Num. of mol.: 2 / Mutation: E131G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0961 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJP7, EC: 1.6.8.-
#2: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPEG1000 AND PEG8000 ARE USED IN THE CRYSTALLIZATION CONDITION OF THIS PROTEIN. THEREFORE IT IS ...PEG1000 AND PEG8000 ARE USED IN THE CRYSTALLIZATION CONDITION OF THIS PROTEIN. THEREFORE IT IS LIKELY THAT THE MODEL OF DODECAETHYLENE GLYCOL IS A PART OF PEG1000 (OR PEG8000).

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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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 1000, 10% PEG 8000, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 20, 2001 / Details: mirrors
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.3→41.53 Å / Num. obs: 62285 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 9.649 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.9
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 8.24 / Num. unique all: 5450 / % possible all: 83.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se-derivatazed HpaC MAD

Resolution: 1.3→41.53 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.216 3139 RANDOM
Rwork0.197 --
all-62277 -
obs-59138 -
Displacement parametersBiso mean: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å2-1.66 Å2
2--0.89 Å20 Å2
3---0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-30 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.3→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 53 400 2713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.9
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 (%)
1.3-1.380.2724700.263883895
1.38-1.490.2595110.24974095
1.49-1.640.2485050.218987895.1
1.64-1.870.2195380.1981005894.9
1.87-2.360.2035700.1861019694.7
2.36-41.530.1975450.181042895.3

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