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- PDB-1wm6: Crystal structure of TT0310 protein from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1wm6
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
Phenylacetic acid degradation protein PaaI
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSugahara, M. / Kunishima, N. / 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 4, 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

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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)114,31310
Polymers114,2428
Non-polymers712
Water7,909439
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)57,1565
Polymers57,1214
Non-polymers351
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-50 kcal/mol
Surface area17590 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)57,1565
Polymers57,1214
Non-polymers351
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-50 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.632, 206.252, 107.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 4.5 Å3/Da / Density % sol: 72.6 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.5
Details: Sodium acetate trihydrate, sodium cacodylate, pH 6.5, Microbatch, temperature 295K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130.0 mg/mlprotein11
250 mM11NaCl
320 mMTris-HCl11pH8.0
41.4 Msodium acetate11
50.1 Mcacodylate-NaOH11pH6.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 0.97925 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 4, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 81420 / Num. obs: 80972 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 43.13 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 3.6 / Num. unique all: 8017 / % possible all: 99.6
Reflection
*PLUS
% possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 99.6 % / Redundancy: 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: 2.4→29.7 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4094 -random
Rwork0.192 ---
obs0.192 80972 99.9 %-
all-81420 --
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1--10.42 Å20 Å20 Å2
2--3.29 Å20 Å2
3---7.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6986 0 2 439 7427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.275 374 -
Rwork0.262 --
obs-7615 100 %
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.7 Å2
LS refinement shell
*PLUS
Rfactor Rwork: 0.267 / Rfactor obs: 0.267

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