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- PDB-6pcb: Crystal structure of beta-ketoadipyl-CoA thiolase mutant (H356A) ... -

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Basic information

Entry
Database: PDB / ID: 6pcb
TitleCrystal structure of beta-ketoadipyl-CoA thiolase mutant (H356A) in complex with COA
ComponentsBeta-ketoadipyl-CoA thiolase
KeywordsTRANSFERASE / Thiolase / aromatic pollutant catabolism / degradative enzymes
Function / homology
Function and homology information


3-oxoadipyl-CoA thiolase / 3-oxoadipyl-CoA thiolase activity / 3,4-dihydroxybenzoate catabolic process
Similarity search - Function
Beta-ketoadipyl CoA thiolase / 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 ...Beta-ketoadipyl CoA thiolase / 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-like
Similarity search - Domain/homology
COENZYME A / Beta-ketoadipyl-CoA thiolase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsSukritee, B. / Panjikar, S.
CitationJournal: J Struct Biol X / Year: 2020
Title: Structural basis for differentiation between two classes of thiolase: Degradative vs biosynthetic thiolase.
Authors: Bhaskar, S. / Steer, D.L. / Anand, R. / Panjikar, S.
History
DepositionJun 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-ketoadipyl-CoA thiolase
B: Beta-ketoadipyl-CoA thiolase
C: Beta-ketoadipyl-CoA thiolase
D: Beta-ketoadipyl-CoA thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,42617
Polymers177,8114
Non-polymers3,61613
Water23,8341323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23630 Å2
ΔGint-107 kcal/mol
Surface area48350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.487, 115.958, 128.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta-ketoadipyl-CoA thiolase


Mass: 44452.645 Da / Num. of mol.: 4 / Mutation: H356A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: pcaF-I, PP_1377 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q88N39, acetyl-CoA C-acyltransferase, 3-oxoadipyl-CoA thiolase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.18 % / Description: Plate type
Crystal growTemperature: 299 K / Method: vapor diffusion / Details: lithium chloride,PEG 6000,tris (pH- 7.3-8.3) / PH range: 7.3-8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.61→80 Å / Num. obs: 413663 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.081 / Net I/σ(I): 11.36
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 65788 / CC1/2: 0.695 / Rrim(I) all: 0.669 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native structure

Resolution: 1.61→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.127 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.08
RfactorNum. reflection% reflectionSelection details
Rfree0.19612 1016 0.5 %RANDOM
Rwork0.16055 ---
obs0.16072 211061 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 22.863 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.61→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11685 0 221 1324 13230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01212329
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.63216739
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6151646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03121.246602
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37152001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.76115106
X-RAY DIFFRACTIONr_chiral_restr0.110.21622
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029438
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6171.9946524
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2523.7278190
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1822.3525805
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.36130.7919346
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 62 -
Rwork0.245 15362 -
obs--99.01 %

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