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- PDB-2f6q: The crystal structure of human peroxisomal delta3, delta2 enoyl C... -

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Basic information

Entry
Database: PDB / ID: 2f6q
TitleThe crystal structure of human peroxisomal delta3, delta2 enoyl CoA isomerase (PECI)
ComponentsPeroxisomal 3,2-trans-enoyl-CoA isomerase
KeywordsISOMERASE / enoyl CoA isomerase / peroxisomes / fatty acid metabolism / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Beta-oxidation of very long chain fatty acids / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle ...Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Beta-oxidation of very long chain fatty acids / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle / mitochondrion / membrane / cytosol
Similarity search - Function
Acyl-CoA-binding protein, ACBP, conserved site / Acyl-CoA-binding (ACB) domain signature. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase ...Acyl-CoA-binding protein, ACBP, conserved site / Acyl-CoA-binding (ACB) domain signature. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / FERM/acyl-CoA-binding protein superfamily / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Enoyl-CoA delta isomerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsTurnbull, A. / Lukacik, P. / Shafqat, N. / Smee, C. / Berridge, G. / Guo, K. / von Delft, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. ...Turnbull, A. / Lukacik, P. / Shafqat, N. / Smee, C. / Berridge, G. / Guo, K. / von Delft, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Gileadi, O. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human peroxisomal delta3, delta2 enoyl CoA isomerase (PECI)
Authors: Turnbull, A. / Lukacik, P. / Shafqat, N. / Smee, C. / Berridge, G. / Guo, K. / von Delft, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Gileadi, O. / Oppermann, U.
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisomal 3,2-trans-enoyl-CoA isomerase
B: Peroxisomal 3,2-trans-enoyl-CoA isomerase
C: Peroxisomal 3,2-trans-enoyl-CoA isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1774
Polymers94,0553
Non-polymers1221
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-39 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.931, 123.196, 128.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: PHE / End label comp-ID: ASN / Refine code: 6 / Auth seq-ID: 109 - 352 / Label seq-ID: 25 - 268

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsThe asymmetric unit contains a biological trimer comprising chains A,B and C

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Components

#1: Protein Peroxisomal 3,2-trans-enoyl-CoA isomerase / Dodecenoyl-CoA isomerase / Delta3 / delta2-enoyl-CoA isomerase / D3 / D2-enoyl-CoA isomerase / DBI- ...Dodecenoyl-CoA isomerase / Delta3 / delta2-enoyl-CoA isomerase / D3 / D2-enoyl-CoA isomerase / DBI-related protein 1 / DRS-1 / Hepatocellular carcinoma-associated antigen 88


Mass: 31351.752 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PECI / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: O75521, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 % isopropanol, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979097 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2005
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979097 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 54609 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 %
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.5 % / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.806 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25728 2769 5.1 %RANDOM
Rwork0.21293 ---
all0.21516 51615 --
obs0.21516 51615 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.902 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2---0.19 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 8 133 5713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225722
X-RAY DIFFRACTIONr_bond_other_d0.0010.023842
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.967767
X-RAY DIFFRACTIONr_angle_other_deg0.88839396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8685742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56623.624218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20115933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1621531
X-RAY DIFFRACTIONr_chiral_restr0.0780.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021159
X-RAY DIFFRACTIONr_nbd_refined0.2210.21249
X-RAY DIFFRACTIONr_nbd_other0.1830.23948
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22934
X-RAY DIFFRACTIONr_nbtor_other0.0870.23006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.2205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.24
X-RAY DIFFRACTIONr_mcbond_it1.071.53780
X-RAY DIFFRACTIONr_mcbond_other0.2031.51493
X-RAY DIFFRACTIONr_mcangle_it1.17625960
X-RAY DIFFRACTIONr_scbond_it2.18132160
X-RAY DIFFRACTIONr_scangle_it3.1934.51803
Refine LS restraints NCS

Ens-ID: 1 / Number: 2797 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.365
2Bloose positional0.395
3Cloose positional0.415
1Aloose thermal1.6610
2Bloose thermal1.4710
3Cloose thermal1.4310
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 218 -
Rwork0.248 3633 -
obs--97.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3655-0.11420.35811.106-0.0011.34910.0347-0.0305-0.1004-0.0414-0.02060.01590.2017-0.0079-0.014-0.07290.00360.0014-0.0361-0.0245-0.111938.386764.974617.2107
20.9657-0.0905-0.38481.08930.24212.06260.01550.08610.071-0.1361-0.06650.1185-0.1486-0.13150.051-0.12430.0228-0.0167-0.0535-0.0084-0.065326.049996.651920.7
30.7310.1969-0.13271.909-0.41691.2428-0.0075-0.09470.06680.3256-0.03720.0513-0.06310.01250.0448-0.0605-0.0155-0.0103-0.01080.0025-0.116536.577578.493348.2475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA108 - 14924 - 65
2X-RAY DIFFRACTION1AA150 - 17866 - 94
3X-RAY DIFFRACTION1AA179 - 30295 - 218
4X-RAY DIFFRACTION1AA303 - 352219 - 268
5X-RAY DIFFRACTION2BB109 - 20825 - 124
6X-RAY DIFFRACTION2BB209 - 292125 - 208
7X-RAY DIFFRACTION2BB293 - 323209 - 239
8X-RAY DIFFRACTION2BB324 - 360240 - 276
9X-RAY DIFFRACTION3CC108 - 13724 - 53
10X-RAY DIFFRACTION3CC138 - 15054 - 66
11X-RAY DIFFRACTION3CC151 - 35767 - 273

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