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- PDB-5f0v: X-ray crystal structure of a thiolase from Escherichia coli at 1.... -

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Basic information

Entry
Database: PDB / ID: 5f0v
TitleX-ray crystal structure of a thiolase from Escherichia coli at 1.8 A resolution
ComponentsAcetyl-CoA acetyltransferase
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 / 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
Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionNov 28, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,57748
Polymers161,8464
Non-polymers2,73144
Water20,4651136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22190 Å2
ΔGint50 kcal/mol
Surface area47350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.930, 75.310, 147.410
Angle α, β, γ (deg.)90.00, 131.42, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
13A
23D
14C
24B
15C
25D
16B
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: -1 - 393 / Label seq-ID: 1 - 395

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12AA
22BB
13AA
23DD
14CC
24BB
15CC
25DD
16BB
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 40461.434 Da / Num. of mol.: 4 / 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: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1136 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 295 K / Method: microbatch / Details: 0.2 M Ammonium fluride 20% (w/v) PEG3350

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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: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→35.6 Å / Num. obs: 135774 / % possible obs: 99 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALA2.2.1data reduction
SCALA2.2.1data scaling
PHASER2.2.21phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E1L

4e1l


Resolution: 1.8→35.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.571 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19537 6673 4.9 %RANDOM
Rwork0.16032 ---
obs0.162 129093 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.293 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20.25 Å2
2---1.02 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.8→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11088 0 175 1136 12399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911415
X-RAY DIFFRACTIONr_bond_other_d0.010.0211327
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.97615378
X-RAY DIFFRACTIONr_angle_other_deg1.538325884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01351593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14225.104384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.082151787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3441553
X-RAY DIFFRACTIONr_chiral_restr0.1380.21841
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213219
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022391
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_it1.3741.6076325
X-RAY DIFFRACTIONr_mcbond_other1.3691.6066324
X-RAY DIFFRACTIONr_mcangle_it1.8412.4017899
X-RAY DIFFRACTIONr_mcangle_other1.8422.4027900
X-RAY DIFFRACTIONr_scbond_it2.21.895090
X-RAY DIFFRACTIONr_scbond_other2.21.895090
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1032.6947470
X-RAY DIFFRACTIONr_long_range_B_refined4.78416.10751536
X-RAY DIFFRACTIONr_long_range_B_other4.78416.10751537
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)
11A234810.08
12C234810.08
21A231820.08
22B231820.08
31A230120.08
32D230120.08
41C234910.07
42B234910.07
51C230210.08
52D230210.08
61B227250.09
62D227250.09
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 421 -
Rwork0.24 8238 -
obs--81.51 %
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)
10.483-0.0345-0.03740.77710.39810.55910.021-0.03350.08530.0789-0.0379-0.0729-0.0256-0.00160.01680.0362-0.031-0.00740.0794-0.00250.033967.2614-27.2925.9845
20.64020.1499-0.05750.8630.29030.6199-0.004-0.04950.08540.018-0.05010.1325-0.14140.00280.05420.0998-0.02670.03280.0182-0.02570.052114.4483-42.148537.881
30.4587-0.2945-0.38250.77110.35351.08780.02140.0957-0.02030.0078-0.081-0.09120.2398-0.02750.05960.09790.00070.02210.0928-0.00410.028967.5648-50.18196.2424
40.99270.466-0.04420.8210.31310.7292-0.0302-0.0462-0.29610.0761-0.0148-0.09420.14720.07370.04510.09170.00450.05870.01240.00830.120623.3595-70.805936.4475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 393
2X-RAY DIFFRACTION2C-1 - 393
3X-RAY DIFFRACTION3B-1 - 393
4X-RAY DIFFRACTION4D-1 - 393

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