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- PDB-2wku: BIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. THE N316H MUTANT. -

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Basic information

Entry
Database: PDB / ID: 2wku
TitleBIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. THE N316H MUTANT.
ComponentsACETYL-COA ACETYLTRANSFERASE
KeywordsTRANSFERASE / ACYLTRANSFERASE / PHB BIOSYNTHESIS / CYTOPLASM / 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, N-terminal / Thiolase, N-terminal domain ...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, N-terminal / Thiolase, N-terminal domain / Thiolase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-mannose / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZOOGLOEA RAMIGERA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMerilainen, G. / Poikela, V. / Kursula, P. / Wierenga, R.K.
CitationJournal: Biochemistry / Year: 2009
Title: The Thiolase Reaction Mechanism: The Importance of Asn316 and His348 for Stabilizing the Enolate Intermediate of the Claisen Condensation.
Authors: Merilainen, G. / Poikela, V. / Kursula, P. / Wierenga, R.K.
History
DepositionJun 18, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)163,84617
Polymers162,2614
Non-polymers1,58513
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16460 Å2
ΔGint-153.2 kcal/mol
Surface area49600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.500, 79.500, 147.700
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.001884, 0.007194), (-0.001877, -1, 0.000869), (0.007195, 0.000856, 1)42.26, -0.7035, -0.245
2given(0.4294, -0.8987, -0.0893), (-0.9022, -0.4313, 0.002142), (-0.04044, 0.07965, -0.996)15.55, 19.09, 69.32
3given(-0.4286, 0.8979, -0.1008), (0.9029, 0.4296, -0.01296), (0.03164, -0.09653, -0.9948)34.31, -18.72, 67.72

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Components

#1: Protein
ACETYL-COA ACETYLTRANSFERASE / ACETOACETYL-COA THIOLASE


Mass: 40565.250 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-11,12-392 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZOOGLOEA RAMIGERA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P07097, acetyl-CoA C-acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Sugar
ChemComp-DNO / D-mannose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 316 TO HIS ENGINEERED RESIDUE IN CHAIN B, ASN 316 TO HIS ...ENGINEERED RESIDUE IN CHAIN A, ASN 316 TO HIS ENGINEERED RESIDUE IN CHAIN B, ASN 316 TO HIS ENGINEERED RESIDUE IN CHAIN C, ASN 316 TO HIS ENGINEERED RESIDUE IN CHAIN D, ASN 316 TO HIS
Sequence detailsA11 INSERTION AND A129R MUTATION WERE FOUND TO EXIST IN THE WILD TYPE CLONE USED AND IS ALREADY ...A11 INSERTION AND A129R MUTATION WERE FOUND TO EXIST IN THE WILD TYPE CLONE USED AND IS ALREADY DESCRIBED IN THE FIRST STRUCTURE PUBLISHED FROM THIS ENZYME, IN THE ARTICLE (STRUCTURE 1999, 7:1279-1290)

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 5.5
Details: 0.95 M LI2SO4, 1.3 (NH4)2SO4, 0.1 M SODIUM CITRATE (PH 5.5), 1 MM EDTA, 1 MM NAN, 1 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 86887 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLU

1dlu


Resolution: 2.3→19.99 Å / SU ML: 1.14 / σ(F): 2 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 4345 5 %
Rwork0.201 --
obs0.204 86886 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.98 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.7842 Å20 Å20.5254 Å2
2---10.6159 Å20 Å2
3----11.2226 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11260 0 93 630 11983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511515
X-RAY DIFFRACTIONf_angle_d0.94415556
X-RAY DIFFRACTIONf_dihedral_angle_d17.0474186
X-RAY DIFFRACTIONf_chiral_restr0.0611737
X-RAY DIFFRACTIONf_plane_restr0.0042053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.26021440.17882726X-RAY DIFFRACTION100
2.3261-2.35340.27681450.19182756X-RAY DIFFRACTION99
2.3534-2.38210.26261410.19182681X-RAY DIFFRACTION100
2.3821-2.41220.28871470.19842792X-RAY DIFFRACTION99
2.4122-2.44390.25261400.19862666X-RAY DIFFRACTION100
2.4439-2.47730.27391460.19092778X-RAY DIFFRACTION100
2.4773-2.51260.27571420.19442695X-RAY DIFFRACTION100
2.5126-2.550.28211470.20362781X-RAY DIFFRACTION100
2.55-2.58980.33731430.20552718X-RAY DIFFRACTION100
2.5898-2.63220.27981450.20882762X-RAY DIFFRACTION100
2.6322-2.67750.31521420.2172704X-RAY DIFFRACTION100
2.6775-2.7260.28761450.21432760X-RAY DIFFRACTION100
2.726-2.77830.2771440.20342719X-RAY DIFFRACTION100
2.7783-2.83490.29321460.20372776X-RAY DIFFRACTION100
2.8349-2.89640.25831430.1992724X-RAY DIFFRACTION100
2.8964-2.96350.27431450.20082756X-RAY DIFFRACTION100
2.9635-3.03740.26051430.19362715X-RAY DIFFRACTION100
3.0374-3.11920.24561460.1922764X-RAY DIFFRACTION100
3.1192-3.21060.2591440.19852751X-RAY DIFFRACTION100
3.2106-3.31380.22211460.19072759X-RAY DIFFRACTION100
3.3138-3.43170.27791440.18762746X-RAY DIFFRACTION100
3.4317-3.56830.21331440.18722732X-RAY DIFFRACTION100
3.5683-3.72980.21641470.17742795X-RAY DIFFRACTION100
3.7298-3.9250.2381430.17642724X-RAY DIFFRACTION100
3.925-4.16880.22751460.17182774X-RAY DIFFRACTION100
4.1688-4.48730.20131460.17132765X-RAY DIFFRACTION100
4.4873-4.93280.21381470.17612794X-RAY DIFFRACTION100
4.9328-5.63250.25751460.20412776X-RAY DIFFRACTION100
5.6325-7.04440.26151470.21742803X-RAY DIFFRACTION100
7.0444-19.98740.2261510.22732849X-RAY DIFFRACTION100
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)
10.2122-0.2297-0.12510.2314-0.02880.0574-0.0293-0.0239-0.0548-0.01050.0387-0.0190.01780.0376-0.0030.01630.0084-0.00380.036-0.00320.075530.5008-12.79567.0119
20.2989-0.43580.11370.3814-0.01730.0165-0.0302-0.05350.04260.03710.05350.01830.0059-0.0261-0.00610.01950.00760.01270.03460.00120.034711.746312.04946.9658
30.1254-0.00740.01560.19220.21930.19170.03920.0221-0.01650.0827-0.028-0.02650.0090.0079-0.00570.29410.0359-0.08410.1975-0.01220.134639.5332-2.896460.0942
40.2578-0.20670.01750.3167-0.17620.14970.0120.1142-0.015-0.0042-0.01080.1284-0.1109-0.0821-0.00720.1420.03580.0180.189-0.01690.07049.02483.223562.957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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