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- PDB-2wl6: BIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. THE N316H-H348N MUTANT. -

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Basic information

Entry
Database: PDB / ID: 2wl6
TitleBIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. THE N316H-H348N 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 / 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: 2.98 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 22, 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 1.2Aug 9, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen
Item: _diffrn_detector.type / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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


Theoretical massNumber of molelcules
Total (without water)162,1654
Polymers162,1654
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13880 Å2
ΔGint-55.2 kcal/mol
Surface area49320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.230, 79.870, 149.920
Angle α, β, γ (deg.)90.00, 92.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.006008, -0.001932), (-0.00601, -1, 0.00143), (-0.001924, 0.001442, 1)42.12, -0.2632, 0.07208
2given(0.4238, -0.9043, -0.05092), (-0.9054, -0.4246, 0.006387), (-0.0274, 0.04339, -0.9987)14.07, 18.98, 69.21
3given(0.4284, -0.9012, -0.06492), (-0.9032, -0.4292, -0.001941), (-0.02612, 0.05947, -0.9979)14.04, 19.03, 69.44

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Components

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


Mass: 40541.207 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) / Variant (production host): PLYSS / References: UniProt: P07097, acetyl-CoA C-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 316 TO HIS ENGINEERED RESIDUE IN CHAIN A, HIS 348 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, ASN 316 TO HIS ENGINEERED RESIDUE IN CHAIN A, HIS 348 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASN 316 TO HIS ENGINEERED RESIDUE IN CHAIN B, HIS 348 TO ASN ENGINEERED RESIDUE IN CHAIN C, ASN 316 TO HIS ENGINEERED RESIDUE IN CHAIN C, HIS 348 TO ASN ENGINEERED RESIDUE IN CHAIN D, ASN 316 TO HIS ENGINEERED RESIDUE IN CHAIN D, HIS 348 TO ASN
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: 6.5
Details: 0.167 M SODIUM CITRATE (PH 6.5), 1.58 M (NH4)2SO4, 1 MM EDTA, 1 MM NAN3 AND 1 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.98→43.9 Å / Num. obs: 39685 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.8
Reflection shellResolution: 2.98→3.14 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.3 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLU

1dlu


Resolution: 2.98→37.42 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.755 / SU B: 22.712 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29059 1974 5 %RANDOM
Rwork0.23208 ---
obs0.235 37217 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.02 Å2
2---0.14 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.98→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11252 0 0 26 11278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211416
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.61.95415420
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14551552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29424.414444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.494151884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8831576
X-RAY DIFFRACTIONr_chiral_restr0.0890.21736
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4831.57636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.896212028
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.07633780
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8644.53392
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.982→3.059 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 141 -
Rwork0.273 2585 -
obs--90.93 %

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