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- PDB-4c2k: Crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase -

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Basic information

Entry
Database: PDB / ID: 4c2k
TitleCrystal structure of human mitochondrial 3-ketoacyl-CoA thiolase
Components3-KETOACYL-COA THIOLASE, MITOCHONDRIALThiolase
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 / 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 / acetyl-CoA C-acetyltransferase activity / fatty acyl-CoA hydrolase activity / Mitochondrial Fatty Acid Beta-Oxidation / Hydrolases; Acting on ester bonds; Thioester hydrolases / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fatty acid beta-oxidation / cholesterol biosynthetic process / cellular response to hypoxia / 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 / Thiolase, C-terminal / Thiolase, C-terminal domain / 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 / Thiolase, C-terminal / Thiolase, C-terminal domain / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / 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 1.2Jul 22, 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_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

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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)178,82030
Polymers176,5824
Non-polymers2,23926
Water8,791488
1
A: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
B: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,52714
Polymers88,2912
Non-polymers1,23712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint10.9 kcal/mol
Surface area27580 Å2
MethodPISA
2
C: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
D: 3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,29316
Polymers88,2912
Non-polymers1,00214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint21 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.730, 196.770, 79.650
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9225, -0.3689, 0.1135), (-0.3587, 0.7107, -0.6052), (0.1426, -0.599, -0.7879)-5.05941, 2.68978, 10.5261
2given(-1, 0.002908, -0.004478), (-0.005051, -0.7871, 0.6168), (-0.001732, 0.6168, 0.7871)10.2605, -73.2041, 25.7465
3given(0.9231, 0.3656, -0.119), (0.3643, -0.9307, -0.03329), (-0.1229, -0.01262, -0.9923)15.3556, -68.612, 35.4807
4given(0.9242, 0.3671, -0.1049), (0.3659, -0.9301, -0.03191), (-0.1093, -0.008907, -0.994)15.2533, -68.6995, 35.6856
5given(-0.9998, -0.00518, -0.01984), (-0.008114, -0.7887, 0.6147), (-0.01883, 0.6148, 0.7885)10.3004, -73.1544, 25.8088
6given(-0.9248, -0.3607, 0.1209), (-0.3598, 0.7258, -0.5863), (0.1238, -0.5857, -0.801)-5.13477, 2.40449, 10.4708

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Components

#1: Protein
3-KETOACYL-COA THIOLASE, MITOCHONDRIAL / Thiolase / 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: 44145.418 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 6.6 / Details: 100 MM MES PH 6.6, 15% MME-PEG5000

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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: TORROIDAL 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→48.17 Å / Num. obs: 109515 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.07
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.07 / % possible all: 99.8

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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→48.17 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.525 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. SOME OR THE SIDE CHAIN ATOMS OF RESIDUES LYS A 38, LYS A 137, LYS A 143, GLU A 177, LYS A 209, LYS A 211, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. SOME OR THE SIDE CHAIN ATOMS OF RESIDUES LYS A 38, LYS A 137, LYS A 143, GLU A 177, LYS A 209, LYS A 211, LYS A 212, LYS A 214, GLN A 226, THR A 228, GLU A 230, LYS A 234, LYS A 241, LYS A 305, LYS A 312, MET B 1, LEU B 4, LYS B 137, LYS B 171, LYS B 173, GLU B 177, GLU B 178, LYS B 209, THR B 210, LYS B 214, GLN B 226, GLN B 233, LYS B 234, LYS B 269, LYS B 270, LYS B 305, LYS B 312, ILE B 338, LYS C 38, LEU C 60, ASN C 131, SER C 140, ASP C 141, GLU C 177, GLU C 178, LYS C 209, THR C 210, LYS C 214, GLN C 215, GLN C 226, GLU C 230, GLN C 233, LYS C 234, LYS C 241, ASP C 242, LYS C 269, ARG C 278, LYS C 305, LYS D 45, GLU D 49, LYS D 109, LYS D 137, LYS D 143, GLN D 158, LYS D 173, LYS D 181, LYS D 209, THR D 210, LYS D 211, LYS D 212, GLN D 215, ARG D 224, GLN D 226, GLU D 230, LYS D 234, LYS D 241, THR D 274, LYS D 305, LYS D 312 HAVE POORLY DEFINED ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22889 5461 5 %RANDOM
Rwork0.19527 ---
obs0.19695 104049 99.65 %-
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 24.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.81 Å2
2---0.28 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 2→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11712 0 140 488 12340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912013
X-RAY DIFFRACTIONr_bond_other_d0.0080.0211839
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.97616198
X-RAY DIFFRACTIONr_angle_other_deg1.191327269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8851577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22624.592453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.998152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2331564
X-RAY DIFFRACTIONr_chiral_restr0.0930.21872
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113593
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022529
X-RAY DIFFRACTIONr_nbd_refined0.2270.23006
X-RAY DIFFRACTIONr_nbd_other0.1780.210648
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25982
X-RAY DIFFRACTIONr_nbtor_other0.0880.26465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.26
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2532.35812013
X-RAY DIFFRACTIONr_mcbond_other0.6112.47411839
X-RAY DIFFRACTIONr_mcangle_it3.3043.4816198
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
Rfree0.252 393 -
Rwork0.222 7738 -
obs--99.91 %

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