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

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Basic information

Entry
Database: PDB / ID: 4jsb
TitleCrystal structure of Tfu_1878, a putative enoyl-CoA hydratase from Thermobifida fusca YX
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / enoyl-CoA hydratase/isomerase family / putative enoyl-CoA hydratase/isomerase
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
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsMikolajczak, K. / Porebski, P.J. / Cooper, D.R. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. / Almo, S.C. ...Mikolajczak, K. / Porebski, P.J. / Cooper, D.R. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. / 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
Authors: Mikolajczak, K. / Porebski, P.J. / Cooper, D.R. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. / Almo, S.C. / Minor, W.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9773
Polymers31,7851
Non-polymers1922
Water6,053336
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)95,9309
Polymers95,3543
Non-polymers5766
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 area11750 Å2
ΔGint-176 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.005, 108.005, 108.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-725-

HOH

21A-735-

HOH

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Components

#1: Protein Enoyl-CoA hydratase


Mass: 31784.535 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M Ammonium sulfate, 0.05M BisTris, 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH) , 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: 21-ID-F / Wavelength: 0.97957 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2013 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.87→38.21 Å / Num. all: 32884 / Num. obs: 32884 / % possible obs: 99.63 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 23.4
Reflection shellResolution: 1.874→1.922 Å / % possible all: 97.02

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Processing

Software
NameVersionClassification
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
SHELXEmodel building
BUCCANEERmodel building
REFMAC5.7.0029refinement
Cootmodel building
FITMUNKrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→38.21 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.314 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.164 1734 5 %RANDOM
Rwork0.14047 ---
all0.14163 32884 --
obs0.14163 32884 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.83 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.87→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 10 336 2242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192010
X-RAY DIFFRACTIONr_bond_other_d0.0050.022023
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9892754
X-RAY DIFFRACTIONr_angle_other_deg0.93834615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40922.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07515321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7511526
X-RAY DIFFRACTIONr_chiral_restr0.1220.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02443
LS refinement shellResolution: 1.874→1.922 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 110 -
Rwork0.235 2329 -
obs-2329 97.02 %
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)
14.8277-3.0325-0.90156.5872.00591.5403-0.09150.01170.07670.08330.2485-0.381-0.07120.2222-0.15710.0789-0.02080.00610.0617-0.04630.046149.06922.37379.374
21.58010.5274-0.40352.24620.57811.1603-0.00670.00960.3276-0.13310.01330.1046-0.2301-0.1005-0.00670.1324-0.00340.00810.0633-0.03340.107942.97120.00372.68
34.69450.0109-3.59630.00910.19298.9082-0.01270.72641.7651-0.0555-0.02380.0734-1.5956-0.91030.03651.07080.0987-0.19310.44470.2851.481236.36931.86360.784
40.8411-0.06340.10070.93410.51381.4348-0.0170.05360.0494-0.02630.02060.037-0.0862-0.0467-0.00350.04030.00930.01080.0217-0.00320.020142.6358.81864.299
52.4849-0.8278-1.28461.3590.42742.42080.0589-0.06530.234-0.01470.0387-0.262-0.10580.0936-0.09750.0496-0.0131-0.01470.0079-0.00350.087662.8573.83568.912
624.99965.329929.03924.81930.02744.07920.8765-0.5672-0.51032.3427-0.5576-0.3179-2.55570.2481-0.31891.3494-0.0201-0.25311.2594-0.44440.590278.8715.52375.937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 30
2X-RAY DIFFRACTION2A31 - 79
3X-RAY DIFFRACTION3A80 - 101
4X-RAY DIFFRACTION4A102 - 211
5X-RAY DIFFRACTION5A212 - 261
6X-RAY DIFFRACTION6A262 - 269

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