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- PDB-1m4t: Biosynthetic thiolase, Cys89 butyrylated -

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Basic information

Entry
Database: PDB / ID: 1m4t
TitleBiosynthetic thiolase, Cys89 butyrylated
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / thiolase fold / butyrylated intermediate
Function / homology
Function and homology information


poly-hydroxybutyrate biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / cytoplasm
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / 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
Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZoogloea ramigera (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsKursula, P. / Ojala, J. / Lambeir, A.-M. / Wierenga, R.K.
CitationJournal: Biochemistry / Year: 2002
Title: The catalytic cycle of biosynthetic thiolase: A conformational journey of an acetyl group through four binding modes and two oxyanion holes
Authors: Kursula, P. / Ojala, J. / Lambeir, A.-M. / Wierenga, R.K.
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / 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

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)163,01410
Polymers162,4454
Non-polymers5686
Water19,6541091
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14780 Å2
ΔGint-103 kcal/mol
Surface area49740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.353, 79.314, 147.324
Angle α, β, γ (deg.)90.00, 93.97, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
Acetyl-CoA acetyltransferase / E.C.2.3.1.9 / Acetoacetyl-CoA thiolase / biosynthetic thiolase


Mass: 40611.301 Da / Num. of mol.: 4 / Mutation: Cys89 butyrylated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoogloea ramigera (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P07097, acetyl-CoA C-acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1091 / 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: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: lithium sulphate, ammonium sulphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP at 293K, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Msodium citrate1reservoirpH5.0
21.0 M1reservoirLi2SO4
30.9 Mammonium sulfate1reservoir
41 mMEDTA1reservoir
51 mMdithiothreitol1reservoir
61 mM1reservoirNaN3
72 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.09785 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09785 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 187197 / Num. obs: 187197 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.097 / Net I/σ(I): 9
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 8928 / Rsym value: 0.344 / % possible all: 95.9
Reflection
*PLUS
Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 95.9 % / Rmerge(I) obs: 0.344

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLU

1dlu


Resolution: 1.77→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.89 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: ISOTROPIC REFINEMENT, TLS PARAMETERISATON
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24209 8647 4.6 %COPIED FROM 1DLU, MISSING RESOLUTION RANGE COMPLETED RANDOMLY
Rwork0.20582 ---
all0.2075 187094 --
obs0.2075 187094 99.16 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.594 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.68 Å2
2---0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.77→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11290 0 32 1091 12413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02111492
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210700
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.95415518
X-RAY DIFFRACTIONr_angle_other_deg0.919324802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41251556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.21744
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213144
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022200
X-RAY DIFFRACTIONr_nbd_refined0.2220.22852
X-RAY DIFFRACTIONr_nbd_other0.2460.213364
X-RAY DIFFRACTIONr_nbtor_other0.0860.26714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2849
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.247
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.2140
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.14147664
X-RAY DIFFRACTIONr_mcangle_it2.892512076
X-RAY DIFFRACTIONr_scbond_it2.74343828
X-RAY DIFFRACTIONr_scangle_it3.84253442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 671
Rwork0.253 12738
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)
10.6455-0.3678-0.010.72940.00440.0992-0.0396-0.0650.00940.06890.0407-0.0138-0.00140.0003-0.00110.0102-0.00010.04080.0261-0.00030.162721.0950.026.804
20.3032-0.14790.16251.33950.27341.30080.054-0.0592-0.00640.623-0.06840.0040.0713-0.12350.01450.83350.1-0.01070.3589-0.0240.369322.9810.27561.817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 3923 - 392
2X-RAY DIFFRACTION1BB3 - 3923 - 392
3X-RAY DIFFRACTION2CC3 - 3923 - 392
4X-RAY DIFFRACTION2DD3 - 3923 - 392
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 178447 / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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