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- PDB-5f38: X-ray crystal structure of a thiolase from Escherichia coli at 1.... -

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Basic information

Entry
Database: PDB / ID: 5f38
TitleX-ray crystal structure of a thiolase from Escherichia coli at 1.8 A resolution
Components(Acetyl-CoA acetyltransferase) x 4
KeywordsTRANSFERASE / E.coli thiolase / fatty acid metabolism / degradative enzyme / active site geometry
Function / homology
Function and homology information


acetoacetic acid catabolic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / protein-containing complex / identical protein binding / cytoplasm
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, C-terminal / Thiolase, C-terminal domain / Thiolase / 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, C-terminal / Thiolase, C-terminal domain / Thiolase / 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
Chem-5UG / COENZYME A / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIthayaraja, M. / Neelanjana, J. / Wierenga, R. / Savithri, H.S. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
DBTBT/IN/FINNISH/27/MRNM/2009 India
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of a thiolase from Escherichia coli at 1.8 angstrom resolution.
Authors: Ithayaraja, M. / Janardan, N. / Wierenga, R.K. / Savithri, H.S. / Murthy, M.R.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
B: Acetyl-CoA acetyltransferase
A: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,16338
Polymers161,5944
Non-polymers3,56834
Water18,6091033
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20850 Å2
ΔGint23 kcal/mol
Surface area45460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.794, 76.254, 266.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22D
13B
23C
14A
24D
15A
25C
16D
26C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B1 - 392
2010A1 - 392
1020B1 - 391
2020D1 - 391
1030B1 - 393
2030C1 - 393
1040A1 - 392
2040D1 - 392
1050A1 - 392
2050C1 - 392
1060D-1 - 392
2060C-1 - 392

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 4 types, 4 molecules BADC

#1: Protein Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase


Mass: 40319.281 Da / Num. of mol.: 1 / Fragment: UNP residues 1-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: atoB, b2224, JW2218 / Production host: Escherichia coli (E. coli) / References: UniProt: P76461, acetyl-CoA C-acetyltransferase
#2: Protein Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase


Mass: 40433.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: atoB, b2224, JW2218 / Production host: Escherichia coli (E. coli) / References: UniProt: P76461, acetyl-CoA C-acetyltransferase
#3: Protein Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase


Mass: 40364.277 Da / Num. of mol.: 1 / Fragment: UNP residues 1-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: atoB, b2224, JW2218 / Production host: Escherichia coli (E. coli) / References: UniProt: P76461, acetyl-CoA C-acetyltransferase
#4: Protein Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase


Mass: 40477.434 Da / Num. of mol.: 1 / Fragment: UNP residues 1-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: atoB, b2224, JW2218 / Production host: Escherichia coli (E. coli) / References: UniProt: P76461, acetyl-CoA C-acetyltransferase

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Non-polymers , 4 types, 1067 molecules

#5: Chemical ChemComp-COZ / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C21H36N7O16P3S / References: acetyl-CoA C-acyltransferase
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-5UG / [(3~{S})-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(2-sulfanylethylamino)propyl]amino]butyl] phosphono hydrogen phosphate


Mass: 438.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H24N2O10P2S / References: acetyl-CoA C-acyltransferase
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1033 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.1 M Bis-tris propane pH 8.0, 35% PEG6000, 0.05 LiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→36.8 Å / Num. obs: 150897 / % possible obs: 99.5 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.0117 / Net I/σ(I): 2.1
Reflection shellHighest resolution: 1.9 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALAdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F0V

5f0v


Resolution: 1.9→36.8 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.998 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23481 5910 5 %RANDOM
Rwork0.19673 ---
obs0.19865 113201 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0 Å20 Å2
2--1.04 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.9→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10760 0 172 1033 11965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01911086
X-RAY DIFFRACTIONr_bond_other_d0.0090.0210797
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.98514961
X-RAY DIFFRACTIONr_angle_other_deg1.326324662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89351559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62925.211355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.936151653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8611545
X-RAY DIFFRACTIONr_chiral_restr0.1110.21776
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212875
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022307
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_it0.7320.9246204
X-RAY DIFFRACTIONr_mcbond_other0.730.9246203
X-RAY DIFFRACTIONr_mcangle_it1.1491.3797739
X-RAY DIFFRACTIONr_mcangle_other1.1491.3797740
X-RAY DIFFRACTIONr_scbond_it1.3471.124882
X-RAY DIFFRACTIONr_scbond_other1.3471.124882
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.91.5967212
X-RAY DIFFRACTIONr_long_range_B_refined6.8529.15913100
X-RAY DIFFRACTIONr_long_range_B_other6.7418.51112734
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B204390.06
12A204390.06
21B228840.05
22D228840.05
31B230930.05
32C230930.05
41A204850.06
42D204850.06
51A204810.06
52C204810.06
61D232850.06
62C232850.06
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 474 -
Rwork0.241 8175 -
obs--99.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1280.30270.16620.25490.56493.95390.19680.0975-0.22390.15310.1032-0.11580.4428-0.0557-0.30010.2136-0.0402-0.06380.1451-0.04020.0679-0.9733.39128.593
20.76760.38040.37910.48810.62283.82740.3012-0.27440.07790.101-0.05330.0054-0.53190.1608-0.24790.3309-0.18440.07870.1932-0.06080.0334-6.689-13.776105.211
30.74010.49230.22211.09950.33761.1370.0317-0.00250.0548-0.1155-0.06750.19290.0709-0.32160.03570.1459-0.0448-0.0460.211-0.00720.039534.88430.07593.22
40.61830.37790.21360.88430.26031.36050.2325-0.2441-0.0560.2559-0.1438-0.17030.03940.1297-0.08870.1896-0.1164-0.0560.21140.01240.037314.09724.54272.01
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 392
2X-RAY DIFFRACTION2B1 - 393
3X-RAY DIFFRACTION3C-1 - 390
4X-RAY DIFFRACTION4D-1 - 392

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