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- PDB-1ou6: Biosynthetic thiolase from Zoogloea ramigera in complex with acet... -

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Basic information

Entry
Database: PDB / ID: 1ou6
TitleBiosynthetic thiolase from Zoogloea ramigera in complex with acetyl-O-pantetheine-11-pivalate
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, 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
PANTOTHENYL-AMINOETHANOL-ACETATE PIVALIC ACID / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZoogloea ramigera (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsKursula, P. / Schmitz, W. / Wierenga, R.K.
CitationJournal: To be Published
Title: The surprising binding mode of a coenzyme A analogue, O-pantetheine-11-pivalate, in the catalytic cavity of bacterial biosynthetic thiolase
Authors: Kursula, P. / Schmitz, W. / Wierenga, R.K.
History
DepositionMar 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / 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)163,39010
Polymers162,2294
Non-polymers1,1616
Water28,0491557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16270 Å2
ΔGint-112 kcal/mol
Surface area49640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.380, 78.950, 148.820
Angle α, β, γ (deg.)90.00, 92.96, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A C
22B D
/ NCS ensembles :
ID
1
2

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Components

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


Mass: 40557.211 Da / Num. of mol.: 4 / Mutation: Cys89 hydroxylated
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-168 / PANTOTHENYL-AMINOETHANOL-ACETATE PIVALIC ACID


Mass: 388.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H32N2O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1557 / 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: 2.73 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, lithium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→20 Å / Num. all: 111939 / Num. obs: 111939 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 2.07→2.2 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 36071 / Rsym value: 0.232 / % possible all: 83.6

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.702 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.158 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21171 4876 4.4 %RANDOM
Rwork0.16081 ---
all0.16307 111938 --
obs0.16307 111938 94.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.895 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å20.01 Å2
2---0.52 Å20 Å2
3---2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.07→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11336 0 74 1557 12967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02111572
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210766
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.95815636
X-RAY DIFFRACTIONr_angle_other_deg0.836324936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29751564
X-RAY DIFFRACTIONr_chiral_restr0.0880.21758
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213244
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022212
X-RAY DIFFRACTIONr_nbd_refined0.2080.22727
X-RAY DIFFRACTIONr_nbd_other0.2440.213628
X-RAY DIFFRACTIONr_nbtor_other0.0870.26890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.21171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.252
X-RAY DIFFRACTIONr_mcbond_it1.93547700
X-RAY DIFFRACTIONr_mcangle_it2.656512136
X-RAY DIFFRACTIONr_scbond_it2.85453872
X-RAY DIFFRACTIONr_scangle_it4.13463500
Refine LS restraints NCS

Number: 5510 / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
11Atight positional0.210.3
22Btight positional0.240.3
11Atight thermal1.9810
22Btight thermal1.9710
LS refinement shellResolution: 2.07→2.125 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 154
Rwork0.232 6430
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)
11.0675-0.6931-0.02350.93290.0120.1965-0.0466-0.0604-0.00060.0810.0544-0.0116-0.0033-0.0029-0.00780.0344-0.01670.00180.04540.00090.013921.098-0.1026.78
20.9958-0.38830.03851.24430.28591.10770.0479-0.0137-0.00670.0893-0.10540.13470.0283-0.14620.05750.30030.0096-0.00610.2344-0.02250.026522.9920.35861.737
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

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