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- PDB-5cpg: R-Hydratase PhaJ1 from Pseudomonas aeruginosa in the unliganded form -

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Basic information

Entry
Database: PDB / ID: 5cpg
TitleR-Hydratase PhaJ1 from Pseudomonas aeruginosa in the unliganded form
Components(R)-specific enoyl-CoA hydratase
KeywordsLYASE / Hotdog fold / four-layered structure / hydratase 2 motif / (R)-hydratase-specific overhang
Function / homology
Function and homology information


enoyl-CoA hydratase 2 / fatty acid synthase complex / hydro-lyase activity / fatty acid synthase activity / fatty acid biosynthetic process
Similarity search - Function
: / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
(R)-specific enoyl-CoA hydratase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.694 Å
AuthorsTsuge, T. / Sato, S. / Hiroe, A. / Ishizuka, K. / Kanazawa, H. / Kanagarajan, S. / Shiro, Y. / Hisano, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS Japan
CitationJournal: Appl.Environ.Microbiol. / Year: 2015
Title: Contribution of the Distal Pocket Residue to the Acyl-Chain-Length Specificity of (R)-Specific Enoyl-Coenzyme A Hydratases from Pseudomonas spp.
Authors: Tsuge, T. / Sato, S. / Hiroe, A. / Ishizuka, K. / Kanazawa, H. / Shiro, Y. / Hisano, T.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: (R)-specific enoyl-CoA hydratase
B: (R)-specific enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,31310
Polymers33,5762
Non-polymers7378
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-36 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.530, 65.721, 77.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein (R)-specific enoyl-CoA hydratase / (R)-Hydratase / (R)-specific trans-2-enoyl-CoA hydratase / PhaJ / hydratase 2 / ECH2


Mass: 16788.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: DSM-1707 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LBK2, enoyl-CoA hydratase 2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15 - 20% PEG 3350, 20% glycerol, 0.1 M Bis-Tris pH 6.0-6.5
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 35882 / % possible obs: 97.5 % / Redundancy: 14 % / Biso Wilson estimate: 13.11 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.02 / Rrim(I) all: 0.075 / Χ2: 0.945 / Net I/av σ(I): 37.311 / Net I/σ(I): 10.7 / Num. measured all: 503743
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.69-1.7210.60.92616280.7060.2880.9730.70589.8
1.72-1.7513.20.87217440.8130.2460.9070.74296.9
1.75-1.7814.40.70617530.8980.1920.7320.78196.4
1.78-1.8214.60.57517480.9230.1540.5950.80696.7
1.82-1.8614.80.44317450.9570.1190.4590.82296.8
1.86-1.914.80.40617610.9750.1090.420.86497.1
1.9-1.9514.70.29517640.9730.0790.3060.96197.2
1.95-214.70.26717700.9830.0720.2770.85997.5
2-2.0614.70.20217880.9870.0540.2090.90997.4
2.06-2.1314.60.16517680.9940.0440.170.93397.5
2.13-2.2114.50.14317910.9950.0390.1490.96297.9
2.21-2.2914.50.13417880.9950.0360.1391.24398.1
2.29-2.414.40.118070.9970.0270.1041.03298.4
2.4-2.5214.40.08517990.9980.0230.0891.0598
2.52-2.6814.30.07518150.9980.020.0781.12298.6
2.68-2.8914.20.06218230.9990.0170.0651.16998.4
2.89-3.1814.10.04818370.9990.0130.051.16799
3.18-3.6413.90.03318680.9990.0090.0340.99799.3
3.64-4.5913.50.023188510.0070.0240.88899.3
4.59-5012.10.02200010.0060.0210.76599.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IQ6

1iq6


Resolution: 1.694→39.345 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 1950 5.64 %
Rwork0.1727 --
obs0.1753 34558 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.694→39.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 48 233 2641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132453
X-RAY DIFFRACTIONf_angle_d1.4633316
X-RAY DIFFRACTIONf_dihedral_angle_d12.568934
X-RAY DIFFRACTIONf_chiral_restr0.072385
X-RAY DIFFRACTIONf_plane_restr0.008434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6943-1.73670.28881130.23861789X-RAY DIFFRACTION74
1.7367-1.78360.27811290.22482171X-RAY DIFFRACTION89
1.7836-1.83610.25271310.2032251X-RAY DIFFRACTION92
1.8361-1.89540.24971320.19352199X-RAY DIFFRACTION90
1.8954-1.96310.27241360.21252242X-RAY DIFFRACTION92
1.9631-2.04170.19351430.17432341X-RAY DIFFRACTION96
2.0417-2.13460.22451370.17422395X-RAY DIFFRACTION97
2.1346-2.24720.25831440.18332344X-RAY DIFFRACTION96
2.2472-2.38790.24251410.18092378X-RAY DIFFRACTION96
2.3879-2.57230.21561390.17532432X-RAY DIFFRACTION98
2.5723-2.83110.20971490.17792447X-RAY DIFFRACTION99
2.8311-3.24060.23351500.16532484X-RAY DIFFRACTION99
3.2406-4.08210.1851490.14532499X-RAY DIFFRACTION99
4.0821-39.35560.1791570.1512636X-RAY DIFFRACTION100

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