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- PDB-1m4s: Biosynthetic thiolase, Cys89 acetylated, unliganded form -

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Basic information

Entry
Database: PDB / ID: 1m4s
TitleBiosynthetic thiolase, Cys89 acetylated, unliganded form
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / thiolase fold / acetylated 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: 1.87 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 1.4Oct 30, 2024Group: 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)163,08612
Polymers162,3334
Non-polymers7538
Water19,7081094
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15410 Å2
ΔGint-106 kcal/mol
Surface area49850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.404, 79.275, 148.479
Angle α, β, γ (deg.)90.00, 92.21, 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: 40583.246 Da / Num. of mol.: 4 / Mutation: C89 acetylated
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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1094 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: lithium sulphate, ammonium sulphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP at 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
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: 1.87→50 Å / Num. all: 158418 / Num. obs: 158418 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.092 / Net I/σ(I): 9.5
Reflection shellResolution: 1.87→1.95 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 17066 / Rsym value: 0.354 / % possible all: 90.1
Reflection
*PLUS
Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 90.1 % / Rmerge(I) obs: 0.354

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Processing

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

1dlu


Resolution: 1.87→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.891 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: ISOTROPIC REFINEMENT, TLS PARAMETERISATION
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24725 7187 4.5 %COPIED FROM 1DLU, MISSING RESOLUTION RANGE COMPLETED RANDOMLY
Rwork0.20591 ---
all0.2078 158300 --
obs0.2078 158300 97.97 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.727 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.86 Å2
2---0.68 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.87→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11344 0 44 1094 12482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02111572
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210760
X-RAY DIFFRACTIONr_angle_refined_deg1.511.95515632
X-RAY DIFFRACTIONr_angle_other_deg0.885324964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43651564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.21764
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213212
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022204
X-RAY DIFFRACTIONr_nbd_refined0.2150.22763
X-RAY DIFFRACTIONr_nbd_other0.2460.213389
X-RAY DIFFRACTIONr_nbtor_other0.0870.26614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2910
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.27747712
X-RAY DIFFRACTIONr_mcangle_it2.94512172
X-RAY DIFFRACTIONr_scbond_it2.98353860
X-RAY DIFFRACTIONr_scangle_it4.10863460
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.401 504
Rwork0.372 9575
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)
10.6534-0.4007-0.01270.73670.00950.0518-0.0421-0.0679-0.00090.07190.04120.002-0.0026-0.00440.00080.0003-0.004-0.00410.08420.00170.222321.12-0.1116.747
20.3426-0.12760.15921.11170.21331.03780.0957-0.0613-0.06090.3681-0.0670.1395-0.0088-0.1605-0.02871.05990.0554-0.2660.4065-0.00330.423123.6140.42961.824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3921 - 392
2X-RAY DIFFRACTION1BB1 - 3921 - 392
3X-RAY DIFFRACTION2CC1 - 3921 - 392
4X-RAY DIFFRACTION2DD1 - 3921 - 392
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 151113 / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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