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- PDB-3hrx: Crystal structure of phenylacetic acid degradation protein PaaG -

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Basic information

Entry
Database: PDB / ID: 3hrx
TitleCrystal structure of phenylacetic acid degradation protein PaaG
ComponentsProbable enoyl-CoA hydratase
KeywordsLYASE / the spiral fold / the crotonase superfamily
Function / homology
Function and homology information


Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable enoyl-CoA hydratase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.85 Å
AuthorsKichise, T. / Hisano, T. / Takeda, K. / Miki, K.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of phenylacetic acid degradation protein PaaG from Thermus thermophilus HB8
Authors: Kichise, T. / Hisano, T. / Takeda, K. / Miki, K.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionJun 23, 2009ID: 3GOW
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable enoyl-CoA hydratase
B: Probable enoyl-CoA hydratase
C: Probable enoyl-CoA hydratase
D: Probable enoyl-CoA hydratase
E: Probable enoyl-CoA hydratase
F: Probable enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)165,3776
Polymers165,3776
Non-polymers00
Water23,1491285
1
A: Probable enoyl-CoA hydratase
B: Probable enoyl-CoA hydratase
C: Probable enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)82,6893
Polymers82,6893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-77 kcal/mol
Surface area27470 Å2
MethodPISA
2
D: Probable enoyl-CoA hydratase
E: Probable enoyl-CoA hydratase
F: Probable enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)82,6893
Polymers82,6893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-74 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.488, 139.368, 156.220
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
Probable enoyl-CoA hydratase / Phenylacetic acid degradation protein PaaG


Mass: 27562.836 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0290 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLK3, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1285 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir solution containing 20% (v/v) PEG MME2000, 0.05M KH2PO4, 5% (v/v) non-detergent sulfobetain (NDSB) 201, and 20% (v/v) glycerol were mixed with protein solution in a 1:1, and ...Details: Reservoir solution containing 20% (v/v) PEG MME2000, 0.05M KH2PO4, 5% (v/v) non-detergent sulfobetain (NDSB) 201, and 20% (v/v) glycerol were mixed with protein solution in a 1:1, and equilibrated against the reservoir solution. , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→42.7 Å / Num. obs: 139053 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 32.8
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.85→42.68 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2890774.36 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: An initial model was obtained from SeMet data. The Se sites for the SeMet data were identified by phasing the SeMet data with SAD phases calculated from osmium data.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 6578 4.7 %random
Rwork0.177 ---
obs-131061 94.2 %-
Solvent computationBsol: 66.668 Å2
Displacement parametersBiso max: 82.35 Å2 / Biso mean: 26.471 Å2 / Biso min: 7.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.205 Å20 Å20 Å2
2--0.111 Å20 Å2
3---0.094 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11399 0 0 1285 12684
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.5241.5
X-RAY DIFFRACTIONc_mcangle_it3.1742
X-RAY DIFFRACTIONc_scbond_it4.0872
X-RAY DIFFRACTIONc_scangle_it5.8182.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 905 5 %
Rwork0.236 17218 -
obs-17218 78.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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