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- PDB-2vu2: Biosynthetic thiolase from Z. ramigera. Complex with S-pantethein... -

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Basic information

Entry
Database: PDB / ID: 2vu2
TitleBiosynthetic thiolase from Z. ramigera. Complex with S-pantetheine-11- pivalate.
ComponentsACETYL-COA ACETYLTRANSFERASE
KeywordsTRANSFERASE / ACYLTRANSFERASE / 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, 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
Chem-PN5 / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZOOGLOEA RAMIGERA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKursula, P. / Merilainen, G. / Schmitz, W. / Wierenga, R.K.
CitationJournal: FEBS J. / Year: 2008
Title: The Sulfur Atoms of the Substrate Coa and the Catalytic Cysteine are Required for a Productive Mode of Substrate Binding in Bacterial Biosynthetic Thiolase, a Thioester-Dependent Enzyme.
Authors: Merilainen, G. / Schmitz, W. / Wierenga, R.K. / Kursula, P.
History
DepositionMay 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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)163,46612
Polymers162,1654
Non-polymers1,3018
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-71 kcal/mol
Surface area60180 Å2
MethodPQS
Unit cell
Length a, b, c (Å)84.320, 79.150, 150.790
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 4 - 392 / Label seq-ID: 4 - 392

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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


Mass: 40541.207 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-392
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-PN5 / (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl 2,2-dimethylpropanoate


Mass: 362.485 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N2O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.05 % / Description: NONE
Crystal growpH: 5 / Details: pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 57985 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.8
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.5 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLU

1dlu


Resolution: 2.65→20 Å / Cor.coef. Fo:Fc: 0.829 / Cor.coef. Fo:Fc free: 0.78 / SU B: 21.26 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.982 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28571 2756 5 %RANDOM
Rwork0.23057 ---
obs0.23331 52345 95.28 %-
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: 64.189 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å2-0.16 Å2
2---1.4 Å20 Å2
3---2.63 Å2
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11252 0 78 528 11858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211486
X-RAY DIFFRACTIONr_bond_other_d0.0010.027646
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.96115520
X-RAY DIFFRACTIONr_angle_other_deg0.889318684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70951552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.624.414444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.428151884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9761576
X-RAY DIFFRACTIONr_chiral_restr0.0690.21742
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022200
X-RAY DIFFRACTIONr_nbd_refined0.1910.22706
X-RAY DIFFRACTIONr_nbd_other0.1830.28476
X-RAY DIFFRACTIONr_nbtor_refined0.1670.25677
X-RAY DIFFRACTIONr_nbtor_other0.0850.26028
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2556
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.04929826
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.378312028
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.95944342
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.70553492
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 4719 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.140.2
2Bmedium positional0.150.2
3Cmedium positional0.140.2
4Dmedium positional0.150.2
1Amedium thermal2.925
2Bmedium thermal3.0925
3Cmedium thermal2.9825
4Dmedium thermal3.2825
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 207
Rwork0.196 3930
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)
11.6111-0.6549-0.14122.04850.01131.1113-0.0736-0.1315-0.1680.1690.08470.05850.1371-0.0814-0.011-0.5954-0.00770.0177-0.5389-0.0101-0.554430.452-12.35927.123
21.434-0.72610.12372.2973-0.04381.1453-0.063-0.12220.16770.17760.0666-0.0602-0.15620.0759-0.0036-0.59-0.010.0338-0.53850.0074-0.569411.735312.38167.1108
30.867-1.08740.63121.419-0.4332.78950.2041-0.0053-0.10230.1443-0.1489-0.4286-0.02090.3982-0.05520.26550.065-0.25450.1024-0.04850.071238.1376-2.639861.3454
40.6905-0.6089-0.54371.43810.81063.0938-0.053-0.2721-0.16220.2893-0.24350.66370.057-0.9230.29650.34070.0595-0.07730.4042-0.05320.20317.82663.566662.8863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 392
2X-RAY DIFFRACTION2B4 - 392
3X-RAY DIFFRACTION3C4 - 392
4X-RAY DIFFRACTION4D4 - 392

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