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- PDB-4omr: Crystal structure of Tfu_1878, a putative enoyl-CoA hydratase fro... -

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Basic information

Entry
Database: PDB / ID: 4omr
TitleCrystal structure of Tfu_1878, a putative enoyl-CoA hydratase from Thermobifida fusca YX in complex with acetoacetyl-CoA
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / hydratase
Function / homology
Function and homology information


delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity / enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid metabolic process / peroxisome
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
BENZAMIDINE / ACETOACETYL-COENZYME A / Enoyl-CoA hydratase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsLangner, K.M. / Cooper, D.R. / Chapman, H.C. / Handing, K.B. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. ...Langner, K.M. / Cooper, D.R. / Chapman, H.C. / Handing, K.B. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of Tfu_1878, a putative enoyl-CoA hydratase from Thermobifida fusca YX in complex with acetoacetyl-CoA
Authors: Langner, K.M. / Cooper, D.R. / Chapman, H.C. / Handing, K.B. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics ...Authors: Langner, K.M. / Cooper, D.R. / Chapman, H.C. / Handing, K.B. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionJan 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9663
Polymers31,9951
Non-polymers9722
Water3,477193
1
A: Enoyl-CoA hydratase
hetero molecules

A: Enoyl-CoA hydratase
hetero molecules

A: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8999
Polymers95,9843
Non-polymers2,9156
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area11660 Å2
ΔGint-60 kcal/mol
Surface area29640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.482, 106.482, 106.482
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-471-

HOH

21A-592-

HOH

DetailsFull trimer is generated by crystallographic symmetry.

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Components

#1: Protein Enoyl-CoA hydratase


Mass: 31994.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_1878 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q47NQ8, enoyl-CoA hydratase
#2: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Ammonium sulfate, 0.05 M BIS-TRIS, 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH), equilibrated against reservoir of 1.5 M NaCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 16, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 34535 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.092 / Χ2: 2.186 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.85-1.887.316921.4661100
1.88-1.927.317311.46411000.883
1.92-1.957.317051.50811000.687
1.95-1.997.416821.50211000.556
1.99-2.047.317111.55411000.487
2.04-2.087.417541.62911000.389
2.08-2.147.416861.66811000.302
2.14-2.197.417181.711000.26
2.19-2.267.417111.74411000.248
2.26-2.337.417071.82411000.202
2.33-2.417.417281.88711000.175
2.41-2.517.417111.96211000.155
2.51-2.627.417112.01511000.137
2.62-2.767.417282.07711000.113
2.76-2.947.417412.15811000.096
2.94-3.167.417232.3611000.08
3.16-3.487.417392.69911000.064
3.48-3.987.317543.02511000.052
3.98-5.027.217753.66911000.048
5.02-406.518286.021199.20.061

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1732 / WRfactor Rwork: 0.1466 / FOM work R set: 0.8985 / SU B: 3.66 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0875 / SU Rfree: 0.0881 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1737 5 %RANDOM
Rwork0.1539 ---
obs0.1553 34441 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.22 Å2 / Biso mean: 31.316 Å2 / Biso min: 17.42 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 63 193 2130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022019
X-RAY DIFFRACTIONr_bond_other_d0.0010.022007
X-RAY DIFFRACTIONr_angle_refined_deg1.9242.0212768
X-RAY DIFFRACTIONr_angle_other_deg0.913.0074578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91823.28873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97515307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.061519
X-RAY DIFFRACTIONr_chiral_restr0.1320.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212291
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_mcbond_it1.4871.5471051
X-RAY DIFFRACTIONr_mcbond_other1.3761.5431049
X-RAY DIFFRACTIONr_mcangle_it1.9732.2971320
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 105 -
Rwork0.234 2418 -
all-2523 -
obs--99.33 %
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)
11.52560.16970.19241.16171.17771.57560.00110.02120.11420.06670.0651-0.065-0.08960.0635-0.06620.1639-0.00830.00260.1029-0.04060.113544.29722.66176.768
22.0265-0.7217-0.03912.0256-0.01280.6535-0.00070.08870.16460.01060.0515-0.2744-0.13330.1574-0.05080.1319-0.02860.01220.0652-0.04460.116450.00821.66871.338
31.3593-0.22350.91934.9042-0.75463.6364-0.11150.04230.3696-0.4097-0.11650.1376-0.448-0.23420.2280.22120.0632-0.02530.123-0.01820.185534.32524.8264.653
40.4237-0.10550.2780.84540.48871.04690.01720.03740.0779-0.03640.00650.0177-0.1511-0.0375-0.02370.13050.00910.01360.0927-0.00790.098242.10710.8461.719
51.6595-0.2817-0.14131.17170.29621.1054-0.0081-0.2050.05310.08480.0258-0.1374-0.02340.0856-0.01770.08160.0119-0.01650.0333-0.00330.044352.6213.57572.877
68.69450.25862.75122.38281.53888.70480.1091-0.28190.6646-0.1995-0.0162-0.5357-0.28610.2439-0.09280.1124-0.0140.05460.09130.00660.287471.6713.40261.641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 38
2X-RAY DIFFRACTION2A39 - 63
3X-RAY DIFFRACTION3A64 - 93
4X-RAY DIFFRACTION4A94 - 199
5X-RAY DIFFRACTION5A200 - 242
6X-RAY DIFFRACTION6A243 - 265

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