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- PDB-2vre: crystal structure of human peroxisomal delta3,5,delta2,4-dienoyl ... -

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Basic information

Entry
Database: PDB / ID: 2vre
Titlecrystal structure of human peroxisomal delta3,5,delta2,4-dienoyl coa isomerase
ComponentsDELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE
KeywordsISOMERASE / FATTY ACID METABOLISM / 4-DIENOYL-COA ISOMERASE / MITOCHONDRION / PHOSPHOPROTEIN / DELTA3 / 5-DELTA2 / PEROXISOME / TRANSIT PEPTIDE / LIPID METABOLISM
Function / homology
Function and homology information


delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / mitochondrion / extracellular exosome / membrane / cytosol
Similarity search - Function
Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase Ech1-like / 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, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase Ech1-like / 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, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYue, W. / Guo, K. / von Delft, F. / Pilka, E. / Murray, J. / Roos, A. / Kochan, G. / Bountra, C. / Arrowsmith, C. / Wikstrom, M. ...Yue, W. / Guo, K. / von Delft, F. / Pilka, E. / Murray, J. / Roos, A. / Kochan, G. / Bountra, C. / Arrowsmith, C. / Wikstrom, M. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Peroxisomal Delta3,5, Delta2,4-Dienoyl Coa Isomerase (Ech1)
Authors: Yue, W. / Guo, K. / von Delft, F. / Pilka, E. / Murray, J. / Roos, A. / Kochan, G. / Bountra, C. / Arrowsmith, C. / Wikstrom, M. / Edwards, A. / Oppermann, U.
History
DepositionMar 31, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 2.0Dec 13, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE
B: DELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE
C: DELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5579
Polymers98,3443
Non-polymers2136
Water7,080393
1
A: DELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE
B: DELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE
C: DELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE
hetero molecules

A: DELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE
B: DELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE
C: DELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,11418
Polymers196,6896
Non-polymers42512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area38930 Å2
ΔGint-189.6 kcal/mol
Surface area63240 Å2
MethodPQS
Unit cell
Length a, b, c (Å)127.580, 137.253, 96.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A26 - 35
2114B26 - 35
3114C26 - 35
1214A39 - 290
2214B39 - 290
3214C39 - 290
1121A95 - 107
2121B95 - 107
3121C95 - 107
1134B22 - 24
2134C22 - 24

NCS ensembles :
ID
1
2
3

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Components

#1: Protein DELTA(3,5)-DELTA(2,4)-DIENOYL-COA ISOMERASE / PEROXISOMAL ENOYL-COENZYME A HYDRATASE-LIKE PROTEIN / ECH1


Mass: 32781.484 Da / Num. of mol.: 3 / Fragment: RESIDUES 50-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PEROXISOME / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3-PRARE2
References: UniProt: Q13011, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-23 FOR CHAINS A,B AND C ARE VECTOR DERIVED SEQUENCE, CONTAINING THE EXPRESSION TAG.

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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: 2.31 Å3/Da / Density % sol: 46.84 % / Description: NONE
Crystal growDetails: 0.2M CA(AC)2, 0.1M CACODYLATE PH 6.5, 18% PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2008
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→93.25 Å / Num. obs: 58508 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DCI

1dci


Resolution: 1.95→93.25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.636 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ADDITIONAL DENSITY IN THE TRIMER INTERFACE WAS MODELLED AS A SET OF UNK ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3132 5.1 %RANDOM
Rwork0.167 ---
obs0.169 58508 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---0.29 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.95→93.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 0 6 393 6404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226157
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9518356
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1045805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18824.115260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.115151027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2761543
X-RAY DIFFRACTIONr_chiral_restr0.1010.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214621
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_it1.70633991
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.64156386
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.71172166
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.799111966
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21A75tight positional0.020.05
22B75tight positional0.030.05
23C75tight positional0.020.05
11A1902medium positional0.210.5
12B1902medium positional0.220.5
13C1902medium positional0.220.5
33A16medium positional0.280.5
21A75tight thermal1.910
22B75tight thermal1.9410
23C75tight thermal3.0310
11A1902medium thermal2.2210
12B1902medium thermal2.2310
13C1902medium thermal2.0810
33A16medium thermal1.5910
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 237
Rwork0.212 4280
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)
12.8904-0.21320.52119.2588-4.83586.8582-0.0114-0.15190.13530.45120.18910.6107-0.1132-0.45-0.1777-0.06210.01760.07340.0393-0.04040.009361.27469.53-34.9312
23.1022-0.26030.62462.3393-0.05192.47560.09670.6124-0.1887-0.5736-0.1196-0.13330.0380.06370.02290.01310.08670.10360.07340.0733-0.108746.90979.1202-29.8012
31.8654.37330.470410.25511.10320.1187-0.01160.00550.0805-0.03490.05310.3960.1572-0.2205-0.04140.2686-0.00190.01420.28380.01590.252727.5438-2.8558-35.4102
49.64647.3041.61396.08351.66380.75760.09730.2567-0.4309-0.25660.0001-0.28570.1802-0.0909-0.0973-0.02240.0497-0.0134-0.00950.0131-0.102132.6561-4.3699-23.297
51.1472-0.2060.55351.1485-0.33911.45380.09240.28450.2083-0.2132-0.0541-0.057-0.09460.0043-0.0383-0.11820.04690.0618-0.1420.0957-0.13940.409615.2185-16.0282
63.1242.18470.844316.5595-7.31184.3824-0.2802-0.1414-0.0053-0.43020.49770.25140.0323-0.043-0.21750.0985-0.00450.02960.1094-0.05180.056842.88929.970228.7135
73.2739-0.3089-0.23561.9251-0.27161.8711-0.0089-0.57140.44270.3630.0353-0.2459-0.18870.351-0.02640.0517-0.0021-0.0241-0.0361-0.16860.044246.269825.822118.0337
81.3829-3.85641.706910.7539-4.75972.10670.28970.0863-0.2282-0.909-0.5537-0.62830.41240.20460.2640.38420.0318-0.00220.3301-0.05040.413264.26512.8679.3503
98.996-8.224-2.75279.22023.07792.6245-0.2019-0.61380.12260.44350.1743-0.1982-0.18620.2690.0276-0.129-0.0564-0.0507-0.14430.0091-0.15952.22627.217410.248
101.5713-0.0701-0.21850.9272-0.00781.02040.0513-0.09750.41890.10960.0035-0.0619-0.2511-0.0205-0.0548-0.09930.01930.0444-0.1995-0.0118-0.029737.216522.65954.7979
116.01456.6314-4.79348.5721-2.4969.9918-0.0958-0.1054-0.0638-0.096-0.0217-0.0139-0.0549-0.36560.11740.12840.0531-0.02660.29890.00240.2307-3.968216.3757-16.9198
122.2801-0.1217-0.23782.57660.43513.53150.0844-0.05170.17140.0043-0.14140.6585-0.0025-0.66030.0571-0.13740.0778-0.02530.19620.04890.14123.010517.0757-6.3918
130.13641.1684-0.950710.0065-8.14216.6251-0.0233-0.3063-0.06120.8142-0.3156-0.379-0.51780.48350.33890.50380.050.02150.5110.02070.42764.71415.043417.2093
141.0307-0.21370.73880.8016-1.88519.57320.0581-0.05360.04530.08290.09460.24740.262-0.4453-0.1528-0.0892-0.00670.03030.00690.01060.002811.76966.97879.5234
150.8827-0.04880.30861.6130.56051.6730.03710.05730.3326-0.1269-0.02040.2468-0.3052-0.3235-0.0167-0.11690.10560.0234-0.06910.06280.014917.856722.1672-6.2712
164.59161.69491.30594.52262.60324.5728-0.03840.3089-0.0207-0.2566-0.05660.38270.0905-0.3490.095-0.11140.036-0.014-0.09320.0587-0.155424.54560.5017-17.6676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 26
2X-RAY DIFFRACTION2A27 - 92
3X-RAY DIFFRACTION3A93 - 107
4X-RAY DIFFRACTION4A108 - 132
5X-RAY DIFFRACTION5A133 - 281
6X-RAY DIFFRACTION6B21 - 26
7X-RAY DIFFRACTION7B27 - 92
8X-RAY DIFFRACTION8B93 - 107
9X-RAY DIFFRACTION9B108 - 132
10X-RAY DIFFRACTION10B133 - 279
11X-RAY DIFFRACTION11C19 - 26
12X-RAY DIFFRACTION12C27 - 92
13X-RAY DIFFRACTION13C93 - 107
14X-RAY DIFFRACTION14C108 - 132
15X-RAY DIFFRACTION15C133 - 254
16X-RAY DIFFRACTION16C255 - 282

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