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

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Basic information

Entry
Database: PDB / ID: 1wlv
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 / COENZYME A / Phenylacetic acid degradation protein PaaI
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJun 29, 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)117,44215
Polymers114,2428
Non-polymers3,2007
Water12,358686
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)58,6917
Polymers57,1214
Non-polymers1,5713
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-55 kcal/mol
Surface area16820 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)58,7508
Polymers57,1214
Non-polymers1,6304
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-55 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.090, 82.583, 59.390
Angle α, β, γ (deg.)90.00, 92.16, 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


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


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 33.7 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.2
Details: Isopropanol, coenzyme A, acetate-NaOH, pH 5.2, Microbatch, temperature 295.0K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130.0 mg/mlprotein11
250 mM11NaCl
35 mM11CoA-SH
427.5 %isopropanol11
50.1 Macetate-NaOH11pH5.2

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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 2, 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: 1.9→30 Å / Num. obs: 66249 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 5.6 / Num. unique all: 13103 / % possible all: 100
Reflection
*PLUS
Redundancy: 7.2 %
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 7 % / Mean I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3355 5.1 %random
Rwork0.17 ---
obs0.17 66249 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.2018 Å2 / ksol: 0.384366 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å21.59 Å2
2---0.55 Å20 Å2
3---1.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6937 0 198 686 7821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.49
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.247 313 4.8 %
Rwork0.212 6256 -
obs--99.1 %
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 5 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.19 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.49
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shell
*PLUS
Num. reflection Rwork: 6569 / Rfactor obs: 0.212

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