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- PDB-1z54: Crystal structure of a hypothetical protein TT1821 from Thermus t... -

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Basic information

Entry
Database: PDB / ID: 1z54
TitleCrystal structure of a hypothetical protein TT1821 from Thermus thermophilus
Componentsprobable thioesterase
KeywordsHYDROLASE / Hypothetical protein / Thermus thermophilus / Structural Genomics / NPPSFA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity
Similarity search - Function
Acyl-CoA thioester hydrolase YbgC/YbaW family / : / Thioesterase-like superfamily / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Probable thioesterase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIhsanawati / Kaminishi, T. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a hypothetical protein TT1821 from Thermus thermophilus
Authors: Ihsanawati / Kaminishi, T. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMar 17, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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: probable thioesterase
B: probable thioesterase
C: probable thioesterase
D: probable thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0077
Polymers60,7304
Non-polymers2763
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-42 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.315, 98.746, 55.339
Angle α, β, γ (deg.)90.00, 112.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
probable thioesterase


Mass: 15182.575 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJV0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.1 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5M Lithium sulfate, 0.1M Sodium hepes buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 60080 / Num. obs: 28489 / % possible obs: 97.4 % / Observed criterion σ(I): 12.9 / Biso Wilson estimate: 15.8 Å2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→33.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1886293.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1382 4.9 %RANDOM
Rwork0.203 ---
obs0.203 28467 97.2 %-
all-28489 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.6644 Å2 / ksol: 0.362952 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å21.04 Å2
2---0.03 Å20 Å2
3---0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 18 422 4676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 230 5 %
Rwork0.247 4370 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GOL.PARAMGOL.TOP

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