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- PDB-2wkt: BIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. COMPLEX OF THE N316A MUTA... -

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Basic information

Entry
Database: PDB / ID: 2wkt
TitleBIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. COMPLEX OF THE N316A MUTANT WITH COENZYME A.
Components(ACETYL-COA ACETYLTRANSFERASE) x 2
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, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / 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 / Thiolase, C-terminal / Thiolase, C-terminal domain / 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: 2 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 / Other / Refinement description / Version format compliance
Revision 1.2Mar 4, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Source and taxonomy
Category: database_PDB_caveat / entity_src_gen ...database_PDB_caveat / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
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)166,07320
Polymers162,0414
Non-polymers4,03216
Water24,1941343
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.600, 79.200, 148.700
Angle α, β, γ (deg.)90.00, 92.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.001988, 0.006402), (-0.00199, -1, -0.000213), (0.006402, -0.000226, 1)42.31, 0.2624, -0.212
2given(0.429, -0.9014, -0.05869), (-0.9024, -0.4305, 0.01602), (-0.0397, 0.04609, -0.9981)14.59, 19.24, 69.16
3given(-0.4305, 0.9007, -0.05872), (0.9021, 0.4315, 0.005767), (0.03053, -0.05049, -0.9983)32.56, -19.05, 67.72

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Components

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Protein , 2 types, 4 molecules ABDC

#1: Protein ACETYL-COA ACETYLTRANSFERASE


Mass: 40514.188 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-11,12-392 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH COA. / Source: (gene. exp.) ZOOGLOEA RAMIGERA (bacteria) / Cell line (production host): BL21(DE3)PLYSS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07097, acetyl-CoA C-acetyltransferase
#2: Protein ACETYL-COA ACETYLTRANSFERASE


Mass: 40498.184 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-11,12-392 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH COA. / Source: (gene. exp.) ZOOGLOEA RAMIGERA (bacteria) / Cell line (production host): BL21(DE3)PLYSS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07097, acetyl-CoA C-acetyltransferase

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Non-polymers , 6 types, 1359 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1343 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 316 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASN 316 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ASN 316 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASN 316 TO ALA ENGINEERED RESIDUE IN CHAIN C, ASN 316 TO ALA ENGINEERED RESIDUE IN CHAIN D, ASN 316 TO ALA
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: 1.9 M (NH4)2SO4, 0.1 M SODIUM CITRATE (PH 6.5), 1 MM EDTA, 1 MM NAN3, 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: Jun 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 132297 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.1 / % possible all: 98.1

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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→19.626 Å / SU ML: 0.42 / σ(F): 1.99 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 6609 5 %
Rwork0.1866 --
obs0.1891 132285 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.217 Å2 / ksol: 0.426 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.1261 Å2-0 Å20.2017 Å2
2---1.5814 Å2-0 Å2
3----1.7361 Å2
Refinement stepCycle: LAST / Resolution: 2→19.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11245 0 240 1343 12828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911711
X-RAY DIFFRACTIONf_angle_d1.18515872
X-RAY DIFFRACTIONf_dihedral_angle_d17.9774377
X-RAY DIFFRACTIONf_chiral_restr0.0821751
X-RAY DIFFRACTIONf_plane_restr0.0062076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.28652180.23614142X-RAY DIFFRACTION99
2.0227-2.04650.29622180.22734137X-RAY DIFFRACTION100
2.0465-2.07140.28352200.22074188X-RAY DIFFRACTION100
2.0714-2.09760.26532180.21014139X-RAY DIFFRACTION100
2.0976-2.12520.26362190.19864171X-RAY DIFFRACTION100
2.1252-2.15430.27132220.20354203X-RAY DIFFRACTION100
2.1543-2.1850.26872160.20054154X-RAY DIFFRACTION100
2.185-2.21760.25092190.18244180X-RAY DIFFRACTION100
2.2176-2.25220.22072190.18054149X-RAY DIFFRACTION100
2.2522-2.2890.25922190.19264177X-RAY DIFFRACTION100
2.289-2.32850.26092190.18924173X-RAY DIFFRACTION100
2.3285-2.37070.25212180.17844152X-RAY DIFFRACTION100
2.3707-2.41620.21842200.17864191X-RAY DIFFRACTION100
2.4162-2.46550.2522200.18574182X-RAY DIFFRACTION100
2.4655-2.5190.24992200.18264171X-RAY DIFFRACTION100
2.519-2.57740.22792190.17444167X-RAY DIFFRACTION100
2.5774-2.64180.26572210.18614205X-RAY DIFFRACTION100
2.6418-2.7130.22642210.1854180X-RAY DIFFRACTION100
2.713-2.79260.24642180.18394148X-RAY DIFFRACTION100
2.7926-2.88250.24652210.17464197X-RAY DIFFRACTION100
2.8825-2.98520.22912210.17664196X-RAY DIFFRACTION100
2.9852-3.10430.23192210.17834198X-RAY DIFFRACTION100
3.1043-3.24490.21292220.17074221X-RAY DIFFRACTION100
3.2449-3.41520.21462200.17324191X-RAY DIFFRACTION100
3.4152-3.62790.23732220.17484214X-RAY DIFFRACTION100
3.6279-3.9060.19472220.17234217X-RAY DIFFRACTION100
3.906-4.29530.18262220.16284221X-RAY DIFFRACTION100
4.2953-4.90830.19332230.16444237X-RAY DIFFRACTION100
4.9083-6.15220.22192240.18334248X-RAY DIFFRACTION100
6.1522-19.62730.21242270.19344327X-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)
10.3041-0.1441-0.04650.2115-0.03120.0298-0.0317-0.009-0.05920.00860.0321-0.0099-0.0072-0.0086-0.001-0.0003-0.0020.00510.0093-0.00280.029230.5498-12.33577.0399
20.3409-0.17320.01420.23530.07230.0426-0.0183-0.02890.0590.02820.03410.00010.00960.0035-0.01090.0069-0.00140.00960.0154-0.0010.025211.676212.39566.991
30.1647-0.0425-0.08140.18560.03040.05370.0502-0.0299-0.02780.0701-0.031-0.0454-0.0308-0.0458-0.01250.21460.0172-0.0770.0796-0.00050.031338.3157-2.985960.328
40.1504-0.0547-0.07650.5246-0.01630.22780.03450.00820.0034-0.0067-0.07070.1686-0.095-0.00110.02080.09030.0172-0.01640.0691-0.0280.03197.97183.290962.2076
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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