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- PDB-1ulq: Crystal structure of tt0182 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1ulq
TitleCrystal structure of tt0182 from Thermus thermophilus HB8
Componentsputative acetyl-CoA acetyltransferase
KeywordsTRANSFERASE / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-ketoadipyl CoA thiolase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAgo, H. / Hamada, K. / Ida, K. / Kanda, H. / Sugahara, M. / Yamamoto, M. / Kuroishi, C. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of tt0182 from Thermus thermophilus HB8
Authors: Ago, H. / Hamada, K. / Ida, K. / Kanda, H. / Sugahara, M. / Yamamoto, M. / Kuroishi, C. / Kuramitsu, S. / Yokoyama, S. / Miyano, M.
History
DepositionSep 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: putative acetyl-CoA acetyltransferase
B: putative acetyl-CoA acetyltransferase
C: putative acetyl-CoA acetyltransferase
D: putative acetyl-CoA acetyltransferase
E: putative acetyl-CoA acetyltransferase
F: putative acetyl-CoA acetyltransferase
G: putative acetyl-CoA acetyltransferase
H: putative acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)342,7048
Polymers342,7048
Non-polymers00
Water00
1
A: putative acetyl-CoA acetyltransferase
B: putative acetyl-CoA acetyltransferase
C: putative acetyl-CoA acetyltransferase
D: putative acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)171,3524
Polymers171,3524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16860 Å2
ΔGint-53 kcal/mol
Surface area49290 Å2
MethodPISA
2
E: putative acetyl-CoA acetyltransferase
F: putative acetyl-CoA acetyltransferase
G: putative acetyl-CoA acetyltransferase
H: putative acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)171,3524
Polymers171,3524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16870 Å2
ΔGint-51 kcal/mol
Surface area49530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.168, 88.873, 164.870
Angle α, β, γ (deg.)90.00, 100.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
putative acetyl-CoA acetyltransferase


Mass: 42837.961 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJM1

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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: 2.91 Å3/Da / Density % sol: 57.4 %
Crystal growMethod: micro batch using tera / Details: micro batch using TERA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Jul 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→74.5 Å / Num. obs: 72562 / % possible obs: 93.6 %
Reflection shellResolution: 3→3.16 Å / % possible all: 86.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DLV

1dlv


Resolution: 3→48.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3665 -RANDOM
Rwork0.218 ---
obs-68885 93.7 %-
Refine analyzeLuzzati coordinate error obs: 0.37 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 3→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23907 0 0 0 23907
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 3→3.02 Å
RfactorNum. reflection
Rfree0.398 70
Rwork0.3473 -
obs-1290

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