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

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Basic information

Entry
Database: PDB / ID: 4jvt
TitleCrystal structure of Tfu_1878, a putative enoyl-CoA hydratase fromThermobifida fusca YX in complex with CoA
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / 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
ACETYL COENZYME *A / ACETATE ION / Enoyl-CoA hydratase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 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 fromThermobifida fusca YX in complex with CoA
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 26, 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)32,8313
Polymers31,9631
Non-polymers8692
Water5,927329
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)98,4949
Polymers95,8883
Non-polymers2,6066
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11680 Å2
ΔGint-68 kcal/mol
Surface area30130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.888, 106.888, 106.888
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-647-

HOH

21A-726-

HOH

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Components

#1: Protein Enoyl-CoA hydratase


Mass: 31962.625 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-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Ammonium acetate, 0.1 M bis-Tris pH 5.5, 25 % PEG 3350, 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: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2013 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→43.67 Å / Num. all: 46157 / Num. obs: 46157 / % possible obs: 99.03 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 27.1
Reflection shellResolution: 1.65→1.693 Å / % possible all: 88.44

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Processing

Software
NameVersionClassification
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
SHELXEmodel building
BUCCANEERmodel building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→43.67 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.072 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15375 2451 5 %RANDOM
Rwork0.13658 ---
all0.13747 46157 --
obs0.13747 46157 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.588 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 52 329 2259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192072
X-RAY DIFFRACTIONr_bond_other_d0.0060.022063
X-RAY DIFFRACTIONr_angle_refined_deg2.0992.012854
X-RAY DIFFRACTIONr_angle_other_deg0.9934718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82722.38184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57215325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.141526
X-RAY DIFFRACTIONr_chiral_restr0.140.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212376
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02461
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 164 -
Rwork0.222 2995 -
obs--88.44 %
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)
14.05250.4006-2.8441.2803-1.80016.2937-0.0205-0.1584-0.06780.0549-0.1858-0.15190.03520.4050.20630.0889-0.0005-0.00380.05420.04740.048322.3571.62750.004
24.32631.07842.21676.67680.37935.25370.0714-0.5754-0.10940.3502-0.11890.3996-0.0592-0.26390.04760.0837-0.01370.04590.10880.04510.07857.2256.68746.801
33.0707-0.6024-1.37611.08520.57344.1196-0.0298-0.2475-0.02560.1328-0.0185-0.1047-0.04530.35280.04830.089-0.0142-0.01720.06570.03790.03923.9867.58147.563
42.9342-0.51320.37855.31761.98157.8058-0.067-0.56710.19040.58330.14320.4581-0.4927-0.5689-0.07610.17960.03870.07410.17450.00420.10356.51313.12148.334
59.7803-19.3472-3.236444.34032.36823.8491-0.3884-0.94770.52341.40641.0876-0.2769-0.32790.5781-0.69910.42540.00960.03830.92-0.18550.451910.12418.07658.676
60.7352-0.2937-0.06181.4694-0.55061.11140.0047-0.07050.04150.1667-0.00970.0676-0.0508-0.02810.0050.042-0.01140.01040.0156-0.00450.014415.56917.97437.319
71.9640.0263-0.22370.9583-0.38231.02090.005-0.0529-0.1753-0.0117-0.03080.00120.12820.09220.02590.07330.01030.00980.0339-0.00080.020626.1247.00629.937
88.2725-1.88210.05179.0914-2.30443.71690.116-0.5689-0.23930.2214-0.15-0.4343-0.04420.51520.03390.0487-0.0349-0.02750.2328-0.00830.049345.32717.41130.416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 29
2X-RAY DIFFRACTION2A30 - 39
3X-RAY DIFFRACTION3A40 - 64
4X-RAY DIFFRACTION4A65 - 84
5X-RAY DIFFRACTION5A85 - 92
6X-RAY DIFFRACTION6A101 - 199
7X-RAY DIFFRACTION7A200 - 242
8X-RAY DIFFRACTION8A243 - 268

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