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

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Basic information

Entry
Database: PDB / ID: 1wlu
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: 1.45 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: Derived calculations / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4083
Polymers14,2801
Non-polymers1282
Water2,882160
1
A: phenylacetic acid degradation protein PaaI
hetero molecules

A: phenylacetic acid degradation protein PaaI
hetero molecules

A: phenylacetic acid degradation protein PaaI
hetero molecules

A: phenylacetic acid degradation protein PaaI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,63112
Polymers57,1214
Non-polymers5108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area9910 Å2
ΔGint-69 kcal/mol
Surface area16570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.804, 76.804, 155.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-1001-

CL

21A-1160-

HOH

31A-1161-

HOH

41A-1162-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by operations: y, x -z; -x, -y, z; -y, -x, -z.

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Components

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


Mass: 14280.224 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 4.02 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5
Details: MPD, sodium citrate, HEPES-NaOH, pH 7.5, Microbatch, temperature 295.0K
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
430 %(v/v)MPD11
50.2 Msodium citrate11
60.1 MHEPES-NaOH11pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 25, 2001 / Details: Mirror
RadiationMonochromator: Si111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→25 Å / Num. all: 41606 / Num. obs: 41591 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.2 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3387 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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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: 1.45→25 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2078 -random
Rwork0.188 ---
obs0.188 41591 100 %-
all-41606 --
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2--1.61 Å20 Å2
3----3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.45→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 7 160 1047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.1
LS refinement shellResolution: 1.45→1.49 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.202 172 -
Rwork0.224 --
obs-3387 100 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.224

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