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- PDB-7mku: Crystal Structure of ENOYL COA-HYDRATASE2 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 7mku
TitleCrystal Structure of ENOYL COA-HYDRATASE2 from Arabidopsis thaliana
ComponentsEnoyl-CoA hydratase 2, peroxisomal
KeywordsLYASE / hydratase / hot-dog fold / PLANT PROTEIN
Function / homology
Function and homology information


fatty acid beta-oxidation, unsaturated, even number / enoyl-CoA hydratase 2 / peroxisome / oxidoreductase activity / lyase activity / mitochondrion
Similarity search - Function
: / MFE-2 hydratase 2 N-terminal domain / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily
Similarity search - Domain/homology
Enoyl-CoA hydratase 2, peroxisomal
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.648 Å
AuthorsPower, S.K. / Korasick, D.A. / Jez, J.M. / Strader, L.C.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136338 United States
National Science Foundation (NSF, United States)IOS-1453750 United States
National Science Foundation (NSF, United States)MCB-1614539 United States
United States Department of Agriculture (USDA)MOW-2014-01877 United States
National Science Foundation (NSF, United States)2011101911 United States
CitationJournal: To Be Published
Title: Crystal Structure of ENOYL COA-HYDRATASE2 from Arabidopsis thaliana
Authors: Korasick, D.A. / Powers, S.K. / Jez, J.M. / Strader, L.C.
History
DepositionApr 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-CoA hydratase 2, peroxisomal
B: Enoyl-CoA hydratase 2, peroxisomal


Theoretical massNumber of molelcules
Total (without water)72,9562
Polymers72,9562
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-6 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.744, 134.744, 127.849
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 16 or (resid 17...
21(chain B and (resid 7 through 193 or resid 195...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUHISHIS(chain A and (resid 7 through 16 or (resid 17...AA7 - 1627 - 36
12LYSLYSLYSLYS(chain A and (resid 7 through 16 or (resid 17...AA1737
13GLUGLUSERSER(chain A and (resid 7 through 16 or (resid 17...AA7 - 30827 - 328
14GLUGLUSERSER(chain A and (resid 7 through 16 or (resid 17...AA7 - 30827 - 328
15GLUGLUSERSER(chain A and (resid 7 through 16 or (resid 17...AA7 - 30827 - 328
21GLUGLUGLUGLU(chain B and (resid 7 through 193 or resid 195...BB7 - 19327 - 213
22THRTHRPROPRO(chain B and (resid 7 through 193 or resid 195...BB195 - 225215 - 245
23PROPROPROPRO(chain B and (resid 7 through 193 or resid 195...BB227247

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Components

#1: Protein Enoyl-CoA hydratase 2, peroxisomal


Mass: 36477.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ECH2, At1g76150, T23E18.38, T23E18.9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VYI3, enoyl-CoA hydratase 2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.9 Å3/Da / Density % sol: 74.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 15% (v/v) reagent alcohol, 100 mM CHES pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.648→40 Å / Num. obs: 38368 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.23 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Χ2: 0.839 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.76.40.82519000.8630.3550.8990.951100
2.7-2.746.40.6219350.9390.2660.6760.853100
2.74-2.86.40.55118740.9220.2370.6010.862100
2.8-2.856.40.45418980.9590.1950.4950.892100
2.85-2.926.40.43319260.9560.1860.4720.85100
2.92-2.986.40.31719280.9760.1360.3450.831100
2.98-3.066.50.29119020.9750.1240.3170.815100
3.06-3.146.50.22619160.9870.0960.2460.831100
3.14-3.236.60.20119070.9840.0840.2180.816100
3.23-3.346.60.15919020.990.0660.1720.784100
3.34-3.466.70.13219300.990.0550.1430.888100
3.46-3.66.90.10819060.9960.0440.1170.891100
3.6-3.7670.09919180.9930.040.1071.073100
3.76-3.967.10.08919380.9930.0360.0961.114100
3.96-4.217.20.0718980.9950.0280.0750.979100
4.21-4.537.40.05719330.9960.0220.0610.964100
4.53-4.987.30.04619250.9980.0180.0490.762100
4.98-5.77.30.04219160.9970.0170.0450.639100
5.7-7.187.50.0419450.9980.0150.0430.559100
7.18-407.40.02819710.9980.0110.0310.50299.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.648→38.897 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.22 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1746 1922 5.48 %
Rwork0.1496 33147 -
obs0.151 35069 91.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.5 Å2 / Biso mean: 42.6272 Å2 / Biso min: 17.25 Å2
Refinement stepCycle: final / Resolution: 2.648→38.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 0 153 4839
Biso mean---40.71 -
Num. residues----603
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2692X-RAY DIFFRACTION6.57TORSIONAL
12B2692X-RAY DIFFRACTION6.57TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.648-2.71410.2922810.2253138054
2.7141-2.78750.28541080.2117179970
2.7875-2.86950.21861330.208209582
2.8695-2.96210.24731390.2089231590
2.9621-3.06790.22871360.196242893
3.0679-3.19070.23281390.1883246195
3.1907-3.33580.21131410.1817253198
3.3358-3.51160.20081480.1612256099
3.5116-3.73140.18561470.1495257399
3.7314-4.01920.15121500.1328257399
4.0192-4.42320.12941490.10962592100
4.4232-5.06210.12661470.10212593100
5.0621-6.37310.15471530.13412615100
6.3731-38.8970.13261510.14182632100
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)
12.3158-0.6284-0.45581.932-0.13922.17890.04190.11070.27840.03-0.0181-0.06260.001-0.0893-0.00520.21560.03030.0070.23050.00520.209137.484150.372660.2734
22.9441-0.21120.34271.13720.32341.8117-0.022-0.09090.29380.03740.0371-0.11140.0460.0164-0.01530.1917-0.00810.02580.2504-0.03050.235913.153361.591980.2177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 308)A7 - 308
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 307)B7 - 307

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