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- PDB-2vu1: Biosynthetic thiolase from Z. ramigera. Complex of with O-panthet... -

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Basic information

Entry
Database: PDB / ID: 2vu1
TitleBiosynthetic thiolase from Z. ramigera. Complex of with O-pantheteine- 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, 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
PANTOTHENYL-AMINOETHANOL-11-PIVALIC ACID / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZOOGLOEA RAMIGERA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsKursula, P. / 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: Refinement description / Version format compliance
Revision 1.2Nov 14, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_residues / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 10, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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)163,42512
Polymers162,2294
Non-polymers1,1968
Water19,7441096
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15190 Å2
ΔGint-59.1 kcal/mol
Surface area60790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.298, 78.737, 148.339
Angle α, β, γ (deg.)90.00, 92.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 392
2114B1 - 392
3114C2 - 392
4114D3 - 392

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Components

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


Mass: 40557.211 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-OPI / PANTOTHENYL-AMINOETHANOL-11-PIVALIC ACID


Mass: 346.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N2O6
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1096 / 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: 2.78 Å3/Da / Density % sol: 55.41 % / 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: BW7A / Wavelength: 0.8416
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8416 Å / Relative weight: 1
ReflectionResolution: 1.51→20 Å / Num. obs: 284637 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.7
Reflection shellResolution: 1.51→1.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.1 / % possible all: 70.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0028refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.782 / SU ML: 0.069 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24726 2742 1 %RANDOM
Rwork0.21543 ---
obs0.21574 271302 92.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.25 Å2
2---0.39 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11311 0 74 1096 12481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02211726
X-RAY DIFFRACTIONr_bond_other_d0.0020.027836
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.96215894
X-RAY DIFFRACTIONr_angle_other_deg1.031319187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0315.0551625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81724.317454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48151935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5791580
X-RAY DIFFRACTIONr_chiral_restr0.110.21793
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022258
X-RAY DIFFRACTIONr_nbd_refined0.220.22843
X-RAY DIFFRACTIONr_nbd_other0.2050.29059
X-RAY DIFFRACTIONr_nbtor_refined0.1780.25819
X-RAY DIFFRACTIONr_nbtor_other0.0930.26465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2939
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.37327768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.997312288
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.76344054
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.90153577
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4519 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.250.3
medium positional0.290
medium positional0.30
medium positional0.320
medium thermal1.555
medium thermal1.490
medium thermal1.670
medium thermal1.690
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.392 133
Rwork0.351 13045
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)
10.767-0.2447-0.0310.801-0.07790.3146-0.0197-0.0457-0.08680.04750.037-0.0220.0326-0.0254-0.0173-0.11970.00160.0164-0.09930.004-0.108530.9258-12.79696.1236
20.7425-0.23980.0720.8940.06860.2819-0.0274-0.03740.08310.05260.0374-0.0256-0.02730.022-0.0099-0.12110.00220.0101-0.1012-0.0021-0.098611.210912.56516.0619
30.5952-0.16670.08961.2198-0.03651.16570.05970.0292-0.02690.1821-0.0331-0.1953-0.01170.115-0.02660.33270.0464-0.12710.1152-0.00770.010738.7631-2.964961.2725
40.7574-0.327-0.13031.65690.49311.45020.05140.0129-0.0880.2888-0.23510.49560.0533-0.46630.18380.32960.02850.00220.2867-0.08620.14037.36013.779763.0355
51.94060.02660.4514.2588-0.25782.0974-0.3207-0.311-0.0090.74880.29760.0434-0.0992-0.09060.02310.17960.1346-0.010.0928-0.0029-0.060121.32030.068334.0973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 129
2X-RAY DIFFRACTION1A1393
3X-RAY DIFFRACTION1A141 - 392
4X-RAY DIFFRACTION2B1 - 129
5X-RAY DIFFRACTION2B1393
6X-RAY DIFFRACTION2B141 - 392
7X-RAY DIFFRACTION3C2 - 129
8X-RAY DIFFRACTION3C141 - 392
9X-RAY DIFFRACTION4D3 - 129
10X-RAY DIFFRACTION4D141 - 392
11X-RAY DIFFRACTION5A130 - 140
12X-RAY DIFFRACTION5B130 - 140
13X-RAY DIFFRACTION5C130 - 140
14X-RAY DIFFRACTION5D130 - 140

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