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- PDB-3lao: Crystal Structure of Enoyl-CoA Hydratase from Pseudomonas aerugin... -

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Basic information

Entry
Database: PDB / ID: 3lao
TitleCrystal Structure of Enoyl-CoA Hydratase from Pseudomonas aeruginosa PA01
Componentsenoyl-CoA hydratase/isomerase
Keywordslyase / isomerase / alpha-beta sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


fatty acid beta-oxidation / cholesterol metabolic process / lyase activity
Similarity search - Function
Enoyl-CoA hydratase, C-terminal / 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 / Alpha Beta
Similarity search - Domain/homology
Enoyl-CoA hydratase EchA19
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKim, Y. / Chhor, G. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Enoyl-CoA Hydratase from Pseudomonas aeruginosa PA01
Authors: Kim, Y. / Chhor, G. / Buck, K. / Joachimiak, A.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: enoyl-CoA hydratase/isomerase
B: enoyl-CoA hydratase/isomerase
C: enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,07010
Polymers84,4253
Non-polymers6457
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-49 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.362, 101.616, 141.536
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 enoyl-CoA hydratase/isomerase


Mass: 28141.637 Da / Num. of mol.: 3 / Fragment: residues 1-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA1240 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9I498
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate, tetrahydrate, 20 % w/v Polyehtlyene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 8, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.4→33.4 Å / Num. all: 28582 / Num. obs: 28582 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 40.52 Å2 / Rsym value: 0.113 / Net I/σ(I): 11.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 5.11 / Num. unique all: 1403 / Rsym value: 0.677 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→33.4 Å / SU ML: 0.36 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2000 7.2 %random
Rwork0.172 ---
all0.177 27781 --
obs0.177 27781 97.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.94 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 48.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.0673 Å2-0 Å2-0 Å2
2---5.1066 Å20 Å2
3----4.9606 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 42 238 5492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145350
X-RAY DIFFRACTIONf_angle_d1.5317230
X-RAY DIFFRACTIONf_dihedral_angle_d19.1941978
X-RAY DIFFRACTIONf_chiral_restr0.094780
X-RAY DIFFRACTIONf_plane_restr0.006967
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4004-2.48610.28641830.2072360254390
2.4861-2.58570.2531920.192476266895
2.5857-2.70330.27181920.1912478267096
2.7033-2.84570.29821950.20732509270496
2.8457-3.02390.29851970.20262547274497
3.0239-3.25720.25842020.19162599280198
3.2572-3.58470.22922050.170326402845100
3.5847-4.10260.20732070.1452668287599
4.1026-5.16570.19462080.125526862894100
5.1657-33.41930.22062190.16662818303799
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.8082-0.38480.34411.23930.25130.5188-0.0258-0.1192-0.04860.07960.07030.0257-0.120.0121-0.04230.1615-0.0282-0.00130.1643-0.01570.135125.438562.79152.403
20.49140.18090.19340.80920.26111.4980.01350.0377-0.0407-0.1332-0.00480.00170.0055-0.15180.00210.10130.02070.02310.1486-0.03650.2064
31.56470.1795-0.0810.95360.4941.34960.0574-0.07940.0530.074-0.12970.0526-0.2008-0.14990.03370.26670.1220.00920.1228-0.00320.1452
Refinement TLS groupSelection details: chain C

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