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- PDB-1m1o: Crystal structure of biosynthetic thiolase, C89A mutant, complexe... -

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Basic information

Entry
Database: PDB / ID: 1m1o
TitleCrystal structure of biosynthetic thiolase, C89A mutant, complexed with acetoacetyl-CoA
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / thiolase fold
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
ACETOACETYL-COENZYME A / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZoogloea ramigera (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionJun 20, 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 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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)164,12410
Polymers162,0374
Non-polymers2,0876
Water18,0511002
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17120 Å2
ΔGint-84 kcal/mol
Surface area49280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.219, 79.219, 148.288
Angle α, β, γ (deg.)90.00, 92.48, 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: 40509.145 Da / Num. of mol.: 4 / Mutation: C89A
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-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1002 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: lithium sulphate, ammonium sulphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP at 295K
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: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 22, 2001
RadiationMonochromator: asymmetrically cut single Si(111) monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 141630 / Num. obs: 141630 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.118 / Net I/σ(I): 7
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 19515 / Rsym value: 0.364 / % possible all: 99.1
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.118
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.364

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Processing

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

1dlu


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.881 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: ISOTROPIC REFINEMENT, TLS PARAMETERISATION
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
Rfree0.25844 6371 4.5 %COPIED FROM PDB ENTRY 1DLU, THE MISSING RESOLUTION RANGE COMPLETED RANDOMLY
Rwork0.21088 ---
all0.213 141522 --
obs0.21307 135151 99.65 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.96 Å2
2---1.8 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11276 0 128 1002 12406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02111580
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210744
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.96415658
X-RAY DIFFRACTIONr_angle_other_deg0.913324906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93951556
X-RAY DIFFRACTIONr_chiral_restr0.0970.21756
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213208
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022216
X-RAY DIFFRACTIONr_nbd_refined0.2170.23059
X-RAY DIFFRACTIONr_nbd_other0.2420.213944
X-RAY DIFFRACTIONr_nbtor_other0.0870.26925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2869
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.224
X-RAY DIFFRACTIONr_mcbond_it2.40847664
X-RAY DIFFRACTIONr_mcangle_it3.018512072
X-RAY DIFFRACTIONr_scbond_it2.57243916
X-RAY DIFFRACTIONr_scangle_it3.48353586
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.28 514
Rwork0.242 9769
obs-9769
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)
10.7656-0.4882-0.01220.89560.00260.0967-0.0436-0.07300.08950.0462-0.0257-0.0024-0.0052-0.00260.0474-0.00970.06770.13630.00170.098621.051-0.0396.962
20.5284-0.08820.14961.48110.00991.08380.0811-0.0366-0.04140.7385-0.0226-0.0603-0.0307-0.1731-0.05851.06450.0517-0.07390.4174-0.02010.243923.3610.33561.577
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 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.211
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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