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- PDB-2cwz: Crystal structure of the Thermus thermophilus hypothetical protei... -

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Basic information

Entry
Database: PDB / ID: 2cwz
TitleCrystal structure of the Thermus thermophilus hypothetical protein TTHA0967, a thioesterase superfamily member
Componentsthioesterase family protein
KeywordsHYDROLASE / Structural genomics / thioesterase / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyFluoroacetyl-CoA thioesterase / Fluoroacetyl-CoA-specific thioesterase / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Thioesterase
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsPioszak, A.A. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the Thermus thermophilus hypothetical protein TTHA0967, a thioesterase superfamily member
Authors: Pioszak, A.A. / Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 27, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 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 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: thioesterase family protein
B: thioesterase family protein
C: thioesterase family protein
D: thioesterase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,88910
Polymers65,5164
Non-polymers3726
Water7,909439
1
A: thioesterase family protein
B: thioesterase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9445
Polymers32,7582
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-20 kcal/mol
Surface area12850 Å2
MethodPISA
2
C: thioesterase family protein
D: thioesterase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9445
Polymers32,7582
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-16 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.501, 114.104, 49.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
thioesterase family protein / hypothetical protein TTHA0967


Mass: 16379.073 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0967 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q5SJP1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, NaHepes, ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9792, 0.9797, 0.9706
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97971
30.97061
ReflectionResolution: 1.85→50 Å / Num. all: 53148 / Num. obs: 53148 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.336 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→45.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2041895.52 / 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
Rfree0.233 2608 5.1 %RANDOM
Rwork0.204 ---
all0.224 50922 --
obs0.204 50922 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1211 Å2 / ksol: 0.437971 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å20 Å20 Å2
2---2.72 Å20 Å2
3---0.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.85→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4431 0 24 439 4894
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_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.742
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.28 250 5.3 %
Rwork0.241 4463 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3edo.paramedo.top

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