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- PDB-1wn3: Crystal structure of TT0310 protein from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1wn3
TitleCrystal structure of TT0310 protein from Thermus thermophilus HB8
Componentsphenylacetic acid degradation protein PaaI
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thioesterase / Hot dog fold / Phenylacetic acid degradation / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acyl-CoA hydrolase activity
Similarity search - Function
Phenylacetic acid degradation protein PaaD / Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HEXANOYL-COENZYME A / Phenylacetic acid degradation protein PaaI
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsKunishima, N. / Sugahara, M. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2005
Title: A Novel Induced-fit Reaction Mechanism of Asymmetric Hot Dog Thioesterase PaaI
Authors: Kunishima, N. / Asada, Y. / Sugahara, M. / Ishijima, J. / Nodake, Y. / Sugahara, M. / Miyano, M. / Kuramitsu, S. / Yokoyama, S. / Sugahara, M.
History
DepositionJul 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: phenylacetic acid degradation protein PaaI
B: phenylacetic acid degradation protein PaaI
C: phenylacetic acid degradation protein PaaI
D: phenylacetic acid degradation protein PaaI
E: phenylacetic acid degradation protein PaaI
F: phenylacetic acid degradation protein PaaI
G: phenylacetic acid degradation protein PaaI
H: phenylacetic acid degradation protein PaaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,83415
Polymers114,2428
Non-polymers3,5937
Water9,980554
1
A: phenylacetic acid degradation protein PaaI
B: phenylacetic acid degradation protein PaaI
C: phenylacetic acid degradation protein PaaI
D: phenylacetic acid degradation protein PaaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8887
Polymers57,1214
Non-polymers1,7673
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-69 kcal/mol
Surface area16590 Å2
MethodPISA
2
E: phenylacetic acid degradation protein PaaI
F: phenylacetic acid degradation protein PaaI
G: phenylacetic acid degradation protein PaaI
H: phenylacetic acid degradation protein PaaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9478
Polymers57,1214
Non-polymers1,8264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-66 kcal/mol
Surface area16950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.055, 82.454, 59.428
Angle α, β, γ (deg.)90.00, 92.49, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a tetramer for instance composed of A, B, C and D subunits in the asymmetric unit.

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Components

#1: Protein
phenylacetic acid degradation protein PaaI / PaaI protein


Mass: 14280.224 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJP3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-HXC / HEXANOYL-COENZYME A


Mass: 865.677 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46N7O17P3S
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 1.87 Å3/Da / Density % sol: 33.6 %
Crystal growTemperature: 295 K / Method: microdialysis / pH: 5.2
Details: Isopropanol, hexanoyl-CoA, acetate-NaOH, pH 5.2, MICRODIALYSIS, temperature 295.0K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130.0 mg/mlprotein11
250 mM11NaCl
32.5 mMhexanoyl-CoA12
413.8 %isopropanol12
50.1 Macetate-NaOH12pH5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 20, 2002 / Details: Mirror
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 48737 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 25.02 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.1 Å / Redundancy: 5 %
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1WLV

1wlv


Resolution: 2.1→30 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2451 5 %random
Rwork0.18 ---
obs0.18 48737 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.4485 Å2 / ksol: 0.382277 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å21.57 Å2
2---2.03 Å20 Å2
3---2.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6951 0 226 554 7731
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.6
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.372.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.281 225 5 %
Rwork0.233 4315 -
obs--92.8 %
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.6
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scangle_it3.372.5
LS refinement shell
*PLUS
Num. reflection Rwork: 4540 / Rfactor obs: 0.233

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