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- PDB-4c2j: Crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase ... -

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Basic information

Entry
Database: PDB / ID: 4c2j
TitleCrystal structure of human mitochondrial 3-ketoacyl-CoA thiolase in complex with CoA
Components3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
KeywordsTRANSFERASE / FATTY ACID METABOLISM / MITOCHONDRIAL BETA-OXIDATION / THIOLYTIC CLEAVAGE
Function / homology
Function and homology information


negative regulation of mitochondrial membrane permeability involved in apoptotic process / acetyl-CoA hydrolase / acetyl-CoA hydrolase activity / palmitoyl-CoA hydrolase / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / acetyl-CoA C-acetyltransferase / fatty acyl-CoA hydrolase activity / Mitochondrial Fatty Acid Beta-Oxidation / acetyl-CoA C-acetyltransferase activity ...negative regulation of mitochondrial membrane permeability involved in apoptotic process / acetyl-CoA hydrolase / acetyl-CoA hydrolase activity / palmitoyl-CoA hydrolase / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / acetyl-CoA C-acetyltransferase / fatty acyl-CoA hydrolase activity / Mitochondrial Fatty Acid Beta-Oxidation / acetyl-CoA C-acetyltransferase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cholesterol biosynthetic process / fatty acid beta-oxidation / cellular response to hypoxia / nuclear body / ciliary basal body / mitochondrial matrix / mitochondrion / RNA binding
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, C-terminal / Thiolase, C-terminal domain / Thiolase / 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, 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 / 3-ketoacyl-CoA thiolase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKiema, T.-R. / Harijan, R.K. / Wierenga, R.K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The Crystal Structure of Human Mitochondrial 3-Ketoacyl-Coa Thiolase (T1): Insight Into the Reaction Mechanism of its Thiolase and Thioesterase Activities
Authors: Kiema, T.-R. / Harijan, R.K. / Strozyk, M. / Fukao, T. / Alexson, S.E.H. / Wierenga, R.K.
History
DepositionAug 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Dec 20, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
B: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
C: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
D: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,70924
Polymers176,6464
Non-polymers4,06320
Water14,538807
1
C: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
D: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,35412
Polymers88,3232
Non-polymers2,03210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-1.9 kcal/mol
Surface area28850 Å2
MethodPISA
2
A: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
B: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,35412
Polymers88,3232
Non-polymers2,03210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-3.1 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.650, 197.160, 79.950
Angle α, β, γ (deg.)90.00, 103.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9215, -0.3709, 0.1153), (-0.3653, 0.7267, -0.5818), (0.132, -0.5783, -0.8051)-5.40895, 2.54391, 10.8397
2given(-0.9999, -0.000276, -0.01045), (-0.00593, -0.8083, 0.5888), (-0.008609, 0.5888, 0.8082)10.4256, -74.6763, 24.5949
3given(-0.924, -0.3644, 0.1158), (-0.3645, 0.7479, -0.5548), (0.1156, -0.5549, -0.8239)-5.14325, 2.60907, 11.7493
4given(0.9228, 0.3703, -0.1068), (0.3684, -0.9289, -0.03751), (-0.1131, -0.004736, -0.9936)15.4612, -69.9121, 35.7033
5given(0.9227, 0.3677, -0.1156), (0.3658, -0.9299, -0.0384), (-0.1216, -0.006841, -0.9926)15.5171, -69.839, 35.5905
6given(-1, 0.002796, -0.002117), (-0.003507, -0.8075, 0.5899), (-6.0E-5, 0.5899, 0.8075)10.3913, -74.6817, 24.5641

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Components

#1: Protein
3-KETOACYL-COA THIOLASE, MITOCHONDRIAL / ACETYL-COA ACYLTRANSFERASE / BETA-KETOTHIOLASE / MITOCHONDRIAL 3-OXOACYL-COA THIOLASE / T1 / 3- ...ACETYL-COA ACYLTRANSFERASE / BETA-KETOTHIOLASE / MITOCHONDRIAL 3-OXOACYL-COA THIOLASE / T1 / 3-KETOACYL-COA THIOLASE


Mass: 44161.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42765, acetyl-CoA C-acyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.19 % / Description: NONE
Crystal growpH: 6.6 / Details: 100 MM MES PH 6.6, 14% MME-PEG 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 17, 2011 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2→46.74 Å / Num. obs: 110210 / % possible obs: 99.8 % / Observed criterion σ(I): 3.72 / Redundancy: 3.8 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.72
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.72 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DM3

1dm3


Resolution: 2→46.74 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.937 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY SOME OF THE SIDECHAIN ATOMS OF RESIDUES HIS A 0, MET A 1, LYS A 109, LYS A 137, LEU A 138, LYS A 143, GLN A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY SOME OF THE SIDECHAIN ATOMS OF RESIDUES HIS A 0, MET A 1, LYS A 109, LYS A 137, LEU A 138, LYS A 143, GLN A 158, GLU A 177, LYS A 181, GLU A 207, LYS A 209, LYS A 214, GLN A 215, ARG A 224, GLN A 226, GLU A 230, LYS A 241, LYS A 305, LYS A 312, ILE A 338, HIS B 0, MET B 1, LYS B 38, LYS B 109, LYS B 137, LYS B 143, LYS B 173, GLU B 177, LYS B 214, GLN B 226, LYS B 234, LYS B 269, LYS B 305, LYS B 312, ILE B 338, HIS C 0, MET C 1, LYS C 143, GLU C 177, LYS C 191, LYS C 209, LYS C 214, GLN C 215, GLN C 226, GLU C 230, LYS C 234, LYS C 241, LYS C 269, LYS C 305, MET D 1, LYS D 38, LYS D 45, GLU D 49, LYS D 109, LYS D 137, LYS D 143, GLN D 158, LYS D 173, LYS D 177, LYS D 209, LYS D 214, GLN D 215, ARG D 224, GLN D 226, GLU D 230, LYS D 234, LYS D 305, LYS D 312 AND ILE D 338 HAVE POORLY DEFINED ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20252 5496 5 %RANDOM
Rwork0.17228 ---
obs0.1738 104693 99.83 %-
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 19.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0.53 Å2
2--0.39 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11673 0 256 807 12736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912117
X-RAY DIFFRACTIONr_bond_other_d0.0070.0211821
X-RAY DIFFRACTIONr_angle_refined_deg1.511.98916383
X-RAY DIFFRACTIONr_angle_other_deg1.1623.00427215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84151571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27924.585458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.097152028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8811564
X-RAY DIFFRACTIONr_chiral_restr0.0890.21892
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113655
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022561
X-RAY DIFFRACTIONr_nbd_refined0.2460.23558
X-RAY DIFFRACTIONr_nbd_other0.1710.211363
X-RAY DIFFRACTIONr_nbtor_refined0.1810.26205
X-RAY DIFFRACTIONr_nbtor_other0.0860.26957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2337
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1030.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9651.85212117
X-RAY DIFFRACTIONr_mcbond_other0.4741.93311821
X-RAY DIFFRACTIONr_mcangle_it3.0322.73416381
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 399 -
Rwork0.186 7721 -
obs--99.95 %

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