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- PDB-6pcd: Crystal structure of beta-ketoadipyl-CoA thiolase mutant (C90S-H3... -

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Basic information

Entry
Database: PDB / ID: 6pcd
TitleCrystal structure of beta-ketoadipyl-CoA thiolase mutant (C90S-H356A) in complex Octanoyl coenzyme A
ComponentsBeta-ketoadipyl-CoA thiolase
KeywordsTRANSFERASE / aromatic pollutant catabolism / degradative enzymes
Function / homology
Function and homology information


3-oxoadipyl-CoA thiolase / 3-oxoadipyl-CoA thiolase activity / acetyl-CoA C-acyltransferase activity / 3,4-dihydroxybenzoate catabolic process / phenylacetate catabolic process / fatty acid beta-oxidation
Similarity search - Function
Beta-ketoadipyl CoA thiolase / 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 ...Beta-ketoadipyl CoA thiolase / 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-like
Similarity search - Domain/homology
COENZYME A / : / OCTANAL / 3-oxoadipyl-CoA thiolase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 1.2Mar 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)180,35722
Polymers177,6824
Non-polymers2,67518
Water31,3281739
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23460 Å2
ΔGint-106 kcal/mol
Surface area48230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.078, 116.621, 128.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-ketoadipyl-CoA thiolase


Mass: 44420.578 Da / Num. of mol.: 4 / Mutation: C90S, 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

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Non-polymers , 6 types, 1757 molecules

#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-OYA / OCTANAL / OCTYL ALDEHYDE / Octanal


Mass: 128.212 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H16O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1739 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.37→80 Å / Num. obs: 677103 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.074 / Net I/σ(I): 11.96
Reflection shellResolution: 1.37→1.45 Å / Redundancy: 3.29 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 108090 / CC1/2: 0.71 / Rrim(I) all: 0.656 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native structure

Resolution: 1.37→19.991 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.138 / SU B: 2.471 / SU ML: 0.042 / Average fsc free: 0.9275 / Average fsc work: 0.9563 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1725 938 0.271 %RANDOM
Rwork0.14 345731 --
all0.14 ---
obs-346669 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 21.824 Å2
Baniso -1Baniso -2Baniso -3
1--1.404 Å20 Å20 Å2
2--3.327 Å20 Å2
3----1.923 Å2
Refinement stepCycle: LAST / Resolution: 1.37→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11649 0 161 1739 13549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212332
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.62916756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49251671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87921.642597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.943152015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.07715101
X-RAY DIFFRACTIONr_chiral_restr0.1020.21622
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029518
X-RAY DIFFRACTIONr_nbd_refined0.2070.26132
X-RAY DIFFRACTIONr_nbtor_refined0.2990.28451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.21232
X-RAY DIFFRACTIONr_metal_ion_refined0.2120.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.231
X-RAY DIFFRACTIONr_mcbond_it1.6881.7776576
X-RAY DIFFRACTIONr_mcangle_it2.1453.3558274
X-RAY DIFFRACTIONr_scbond_it2.8812.1225756
X-RAY DIFFRACTIONr_scangle_it3.433.8528479
X-RAY DIFFRACTIONr_lrange_it3.8128.65419384
X-RAY DIFFRACTIONr_rigid_bond_restr4.231312332
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.37-1.4050.352870.278249570.278254120.6850.85698.55190.273
1.405-1.4440.269670.22246910.22247960.8960.90599.84670.209
1.444-1.4850.205630.192239720.192241080.9440.93799.69720.178
1.485-1.5310.183540.18233870.18234520.9180.94899.95310.164
1.531-1.5810.204540.156226560.156227380.9210.95999.87690.139
1.581-1.6360.168420.127219510.127220030.9610.97599.95460.11
1.636-1.6970.157620.116211880.116212600.9550.97799.9530.098
1.697-1.7660.153810.103203840.103204890.9710.98199.88290.087
1.766-1.8440.156530.098195630.099196610.9720.98299.77110.085
1.844-1.9330.152420.106187420.106188250.9750.9899.78220.095
1.933-2.0360.14380.118178450.118179240.9690.9899.77130.11
2.036-2.1590.159510.133169180.133169870.9790.97699.8940.128
2.159-2.3060.173380.132159290.132159950.9540.97299.82490.13
2.306-2.4880.146360.129148650.129149490.9620.96999.67890.13
2.488-2.7210.183480.133136650.133137900.9550.96999.44160.138
2.721-3.0350.205250.146124140.146125290.9360.96499.28170.156
3.035-3.4910.193300.148110050.148111380.9510.97299.07520.164
3.491-4.2440.17270.13794420.13795150.980.97999.51660.157
4.244-5.870.131290.13775150.13775460.9750.97699.97350.166
5.87-19.9910.127110.16746040.16746180.980.96799.9350.207

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