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- PDB-2vtz: Biosynthetic thiolase from Z. ramigera. Complex of the C89A mutan... -

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Basic information

Entry
Database: PDB / ID: 2vtz
TitleBiosynthetic thiolase from Z. ramigera. Complex of the C89A mutant with coenzyme A.
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
COENZYME A / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZOOGLOEA RAMIGERA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKursula, P. / Merilainen, G. / 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_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_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)165,68314
Polymers162,0374
Non-polymers3,64710
Water14,502805
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15480 Å2
ΔGint-83.5 kcal/mol
Surface area60450 Å2
MethodPQS
Unit cell
Length a, b, c (Å)84.220, 79.570, 148.920
Angle α, β, γ (deg.)90.00, 92.10, 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
1114A1 - 392
2114B1 - 392
3114C1 - 392
4114D1 - 392

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Components

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


Mass: 40509.145 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-392 / Mutation: YES
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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#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.: 805 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 89 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 89 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 89 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 89 TO ALA ENGINEERED RESIDUE IN CHAIN C, CYS 89 TO ALA ENGINEERED RESIDUE IN CHAIN D, CYS 89 TO ALA

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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: 2.9 Å3/Da / Density % sol: 57.2 % / 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: 2.3→20 Å / Num. obs: 87692 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.8 / % possible all: 86.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M3Z

1m3z


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.841 / SU B: 13.354 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26245 4262 5 %RANDOM
Rwork0.22206 ---
obs0.22407 80970 97.37 %-
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: 36.916 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å2-0.61 Å2
2---1.47 Å20 Å2
3---2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11248 0 222 805 12275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211636
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210760
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.97615752
X-RAY DIFFRACTIONr_angle_other_deg0.778324940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56551552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45624.414444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23151880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4691576
X-RAY DIFFRACTIONr_chiral_restr0.0660.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022200
X-RAY DIFFRACTIONr_nbd_refined0.1940.22778
X-RAY DIFFRACTIONr_nbd_other0.1780.211676
X-RAY DIFFRACTIONr_nbtor_refined0.1640.25747
X-RAY DIFFRACTIONr_nbtor_other0.0820.26672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2783
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.65829840
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.821312024
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.26744504
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.81553728
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: 5475 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.140.2
2Bmedium positional0.180.2
3Cmedium positional0.140.2
4Dmedium positional0.150.2
1Amedium thermal1.3310
2Bmedium thermal1.3810
3Cmedium thermal1.310
4Dmedium thermal1.2110
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 269
Rwork0.217 5116
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)
11.448-0.4732-0.15251.94070.06780.5297-0.0509-0.1318-0.13650.17190.0643-0.06680.0624-0.0137-0.0134-0.28420.00080.0034-0.2065-0.0018-0.219930.4273-12.37857.0268
21.3971-0.52510.02872.0068-0.16390.4986-0.0603-0.12170.1520.17070.07760.0346-0.06220.0062-0.0174-0.2874-0.00160.036-0.209-0.0074-0.21511.708512.39847.0206
31.0446-0.69280.48770.7806-0.08271.67840.15740.0444-0.04480.1799-0.1147-0.34190.00030.1673-0.04270.75840.0314-0.22120.2822-0.0150.019138.8448-2.847260.5742
40.5196-0.3137-0.5042.7670.33972.35790.018-0.05570.02210.2938-0.20541.14660.1176-0.5230.18750.82060.0318-0.06760.4433-0.05220.29668.61683.542262.4161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 392
2X-RAY DIFFRACTION1A1393
3X-RAY DIFFRACTION2B1 - 392
4X-RAY DIFFRACTION2B1393
5X-RAY DIFFRACTION3C1 - 392
6X-RAY DIFFRACTION3C1393
7X-RAY DIFFRACTION4D1 - 392
8X-RAY DIFFRACTION4D1393

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