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- PDB-4u4e: Crystal structure of putative thiolase from Sphaerobacter thermop... -

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Basic information

Entry
Database: PDB / ID: 4u4e
TitleCrystal structure of putative thiolase from Sphaerobacter thermophilus DSM 20745
ComponentsThiolase
KeywordsTRANSFERASE / thiolase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Thiolase C-terminal domain-like / Thiolase, C-terminal domain / Thiolase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChang, C. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of putative thiolase from Sphaerobacter thermophilus DSM 20745
Authors: Chang, C. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiolase


Theoretical massNumber of molelcules
Total (without water)40,8301
Polymers40,8301
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.540, 75.540, 123.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsbiological unit is the same as asym.

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Components

#1: Protein Thiolase


Mass: 40829.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / S 6022 / Gene: Sthe_0538 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1C159
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.7 M tir-Sodium Citrate 0.1 M Bis-Tris Propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21397 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.711 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
HKL-3000phasing
Cootmodel building
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.2→34.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 13.316 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.192
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1012 5.1 %RANDOM
Rwork0.172 ---
obs0.174 19886 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 0 50 2695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192701
X-RAY DIFFRACTIONr_bond_other_d0.0010.022575
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.9643670
X-RAY DIFFRACTIONr_angle_other_deg0.70835917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87123.365104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.715412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6221518
X-RAY DIFFRACTIONr_chiral_restr0.0580.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5883.7171442
X-RAY DIFFRACTIONr_mcbond_other3.5813.7161441
X-RAY DIFFRACTIONr_mcangle_it4.3245.5541799
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.98435275
X-RAY DIFFRACTIONr_sphericity_free26.472517
X-RAY DIFFRACTIONr_sphericity_bonded10.30455259
LS refinement shellResolution: 2.2→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 41 -
Rwork0.206 735 -
obs--49.9 %

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