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- PDB-1wdk: fatty acid beta-oxidation multienzyme complex from Pseudomonas fr... -

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Basic information

Entry
Database: PDB / ID: 1wdk
Titlefatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2)
Components
  • 3-ketoacyl-CoA thiolase
  • Fatty oxidation complex alpha subunit
KeywordsLYASE / OXIDOREDUCTASE/TRANSFERASE / alpha2beta2 heterotetrameric complex / OXIDOREDUCTASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / acetyl-CoA C-acyltransferase / Delta3-Delta2-enoyl-CoA isomerase / acetyl-CoA C-acyltransferase activity / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase ...fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / acetyl-CoA C-acyltransferase / Delta3-Delta2-enoyl-CoA isomerase / acetyl-CoA C-acyltransferase activity / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / phenylacetate catabolic process / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / cytoplasm
Similarity search - Function
Fatty oxidation complex, alpha subunit FadB / Acetyl-CoA C-acyltransferase FadA / : / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / : / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain ...Fatty oxidation complex, alpha subunit FadB / Acetyl-CoA C-acyltransferase FadA / : / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / : / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / 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 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-ketoacyl-CoA thiolase / Fatty acid oxidation complex subunit alpha
Similarity search - Component
Biological speciesPseudomonas fragi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsIshikawa, M. / Tsuchiya, D. / Oyama, T. / Tsunaka, Y. / Morikawa, K.
Citation
Journal: Embo J. / Year: 2004
Title: Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex
Authors: Ishikawa, M. / Tsuchiya, D. / Oyama, T. / Tsunaka, Y. / Morikawa, K.
#1: Journal: Biochem.J. / Year: 1997
Title: Reconstitution, morphology and crystallization of a fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi
Authors: Ishikawa, M. / Mikami, Y. / Usukura, J. / Iwasaki, H. / Shinagawa, H. / Morikawa, K.
History
DepositionMay 17, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty oxidation complex alpha subunit
B: Fatty oxidation complex alpha subunit
C: 3-ketoacyl-CoA thiolase
D: 3-ketoacyl-CoA thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,32515
Polymers237,5104
Non-polymers4,81511
Water17,529973
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20400 Å2
ΔGint-179 kcal/mol
Surface area76660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.705, 94.578, 160.001
Angle α, β, γ (deg.)90.00, 111.45, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a heterotetramer as observed in the asymmetric unit.

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Fatty oxidation complex alpha subunit / fatty acid beta-oxidation multienzyme complex / alpha subunit


Mass: 77232.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fragi (bacteria) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): MIF100
References: UniProt: P28793, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase, 3-hydroxybutyryl-CoA epimerase
#2: Protein 3-ketoacyl-CoA thiolase / fatty acid beta-oxidation multienzyme complex / beta subunit / Fatty oxidation complex beta subunit ...fatty acid beta-oxidation multienzyme complex / beta subunit / Fatty oxidation complex beta subunit / Beta-ketothiolase / Acetyl-CoA acyltransferase


Mass: 41522.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fragi (bacteria) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): MIF100 / References: UniProt: P28790, acetyl-CoA C-acyltransferase

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Non-polymers , 6 types, 984 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-N8E / 3,6,9,12,15-PENTAOXATRICOSAN-1-OL / N-OCTYLPENTAOXYETHYLENE / PENTAETHYLENE GLYCOL MONOOCTYL ETHER / OCTYLPENTAGLYCOL N-OCTYLPENTAOXYETHYLENE


Mass: 350.491 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H38O6 / Comment: C8E5, detergent*YM
#6: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#7: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 973 / 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: 2.68 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000, MES, ZnCl2, n-octylpentaoxyethylene, NAD+, acetoacetyl-CoA, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 6, 2002
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 82900 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.7 / % possible all: 80.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2443 5866 random
Rwork0.2026 --
all0.2056 82732 -
obs0.2056 82732 -
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16439 0 289 973 17701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007138
X-RAY DIFFRACTIONc_angle_deg1.24161
X-RAY DIFFRACTIONc_dihedral_angle_d23.05308
X-RAY DIFFRACTIONc_improper_angle_d0.8162
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection
Rfree0.3334 448
Rwork0.2721 -
obs-6400

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