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- PDB-2wl4: BIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. COMPLEX OF THE H348A MUTA... -

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Basic information

Entry
Database: PDB / ID: 2wl4
TitleBIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. COMPLEX OF THE H348A MUTANT WITH COENZYME A.
Components(ACETYL-COA ACETYLTRANSFERASE) x 4
KeywordsTRANSFERASE / ACYLTRANSFERASE / CYTOPLASM / PHB BIOSYNTHESIS / 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
COENZYME A / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZOOGLOEA RAMIGERA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / Refinement description / Version format compliance
Revision 1.2Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.3Dec 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_conn / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET 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)166,10537
Polymers161,9934
Non-polymers4,11233
Water21,0781170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20220 Å2
ΔGint-358.7 kcal/mol
Surface area49520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.310, 79.140, 149.410
Angle α, β, γ (deg.)90.00, 92.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.002366, 0.005677), (-0.002368, -1, -0.000242), (0.005676, -0.000256, 1)42.17, -0.3765, -0.2026
2given(-0.4292, 0.9014, -0.05732), (0.9029, 0.4298, -0.001042), (0.0237, -0.05221, -0.9984)33.34, -18.86, 67.52
3given(-0.425, 0.9011, -0.08588), (0.9043, 0.4268, 0.002921), (0.03929, -0.07642, -0.9963)33.69, -18.95, 67.37

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Components

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Protein , 4 types, 4 molecules ABCD

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


Mass: 40506.141 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-11,12-392 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SUBUNITS A AND B COMPLEXED WITH COA. / 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: Protein ACETYL-COA ACETYLTRANSFERASE / ACETOACETYL-COA THIOLASE


Mass: 40522.145 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-11,12-392 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SUBUNITS A AND B COMPLEXED WITH COA. / 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
#3: Protein ACETYL-COA ACETYLTRANSFERASE / ACETOACETYL-COA THIOLASE


Mass: 40474.141 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-11,12-392 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SUBUNITS A AND B COMPLEXED WITH COA. / 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
#4: Protein ACETYL-COA ACETYLTRANSFERASE / ACETOACETYL-COA THIOLASE


Mass: 40490.145 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-11,12-392 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SUBUNITS A AND B COMPLEXED WITH COA. / 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

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Non-polymers , 5 types, 1203 molecules

#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1170 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 348 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 348 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, HIS 348 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 348 TO ALA ENGINEERED RESIDUE IN CHAIN C, HIS 348 TO ALA ENGINEERED RESIDUE IN CHAIN D, HIS 348 TO ALA
Has protein modificationY
Nonpolymer detailsCOENZYME A (COA): IN SUBUNITS A AND B
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: 61 % / Description: NONE
Crystal growpH: 5.5
Details: 0.95 M LI2SO4, 1.2 M (NH4)2SO4, 0.1 M SODIUM CITRATE (PH 5.5), 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 CCD / Detector: CCD / Date: Jun 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 181049 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

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Processing

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

1dlu


Resolution: 1.8→19.613 Å / SU ML: 0.46 / σ(F): 1.99 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 9051 5 %
Rwork0.2307 --
obs0.2327 180999 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86.405 Å2 / ksol: 0.456 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.5476 Å20 Å20.6161 Å2
2---3.6011 Å20 Å2
3----3.1151 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11238 0 227 1170 12635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811709
X-RAY DIFFRACTIONf_angle_d1.13215872
X-RAY DIFFRACTIONf_dihedral_angle_d17.3394237
X-RAY DIFFRACTIONf_chiral_restr0.0761770
X-RAY DIFFRACTIONf_plane_restr0.0062079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.30892970.25095634X-RAY DIFFRACTION99
1.8205-1.84190.2863000.24365700X-RAY DIFFRACTION99
1.8419-1.86430.292980.24275663X-RAY DIFFRACTION99
1.8643-1.88790.28072970.23255651X-RAY DIFFRACTION99
1.8879-1.91270.26752990.21885664X-RAY DIFFRACTION99
1.9127-1.93890.28853020.21895739X-RAY DIFFRACTION100
1.9389-1.96660.2353010.20635729X-RAY DIFFRACTION100
1.9666-1.99590.26732990.2125681X-RAY DIFFRACTION100
1.9959-2.0270.253010.21065723X-RAY DIFFRACTION100
2.027-2.06020.26913010.20695716X-RAY DIFFRACTION100
2.0602-2.09570.25933010.21285705X-RAY DIFFRACTION100
2.0957-2.13380.24723030.21085775X-RAY DIFFRACTION100
2.1338-2.17480.27452990.22355663X-RAY DIFFRACTION100
2.1748-2.21910.24363030.20735758X-RAY DIFFRACTION100
2.2191-2.26730.24633030.20635762X-RAY DIFFRACTION100
2.2673-2.320.25182990.20325684X-RAY DIFFRACTION100
2.32-2.37790.26593010.20555721X-RAY DIFFRACTION100
2.3779-2.44210.26083020.20485731X-RAY DIFFRACTION100
2.4421-2.51380.24923040.20575772X-RAY DIFFRACTION100
2.5138-2.59470.24913020.21085738X-RAY DIFFRACTION100
2.5947-2.68730.26293030.21485763X-RAY DIFFRACTION100
2.6873-2.79460.24453010.20655723X-RAY DIFFRACTION100
2.7946-2.92140.24333030.21355761X-RAY DIFFRACTION100
2.9214-3.07480.27063010.22785714X-RAY DIFFRACTION100
3.0748-3.26660.26383030.22515767X-RAY DIFFRACTION100
3.2666-3.51750.2553050.22865781X-RAY DIFFRACTION100
3.5175-3.86910.26273020.22245752X-RAY DIFFRACTION100
3.8691-4.42330.24543060.23165800X-RAY DIFFRACTION100
4.4233-5.55190.28993050.25235795X-RAY DIFFRACTION100
5.5519-19.61460.31843100.28395883X-RAY DIFFRACTION99
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)
10.2106-0.2048-0.0480.35-0.00780.0326-0.0266-0.0041-0.02920.00180.0289-0.0163-0.015-0.008-0.00250.02230.0001-0.00450.02760.00150.014430.5068-12.59387.0993
20.2411-0.1970.04630.37250.11180.1216-0.0233-0.01090.01890.03030.02410.02120.01710.01290.00280.0066-0.00050.00070.0097-0.00090.006111.648312.12156.9643
30.07570.0697-0.09330.8544-0.04620.18880.1010.0449-0.09840.698-0.081-0.5829-0.1045-0.0326-0.00510.68850.076-0.50590.1223-0.0160.417338.8313-3.110560.1787
40.39940.3357-0.15251.4479-0.41160.12450.0866-0.23630.07150.917-0.07310.0985-0.14780.1426-0.08930.54340.11510.1180.2915-0.0609-0.00088.75423.242862.4994
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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