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- PDB-2ppy: Crystal structure of Enoyl-CoA hydrates (gk_1992) from Geobacillu... -

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Basic information

Entry
Database: PDB / ID: 2ppy
TitleCrystal structure of Enoyl-CoA hydrates (gk_1992) from Geobacillus Kaustophilus HTA426
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / BETA-OXIDATION / COA / ENOYL-COA HYDRATASE / FATTY ACID METABOLISM / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity
Similarity search - Function
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 ...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
DI(HYDROXYETHYL)ETHER / Enoyl-CoA hydratase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.16 Å
AuthorsKanaujia, S.P. / Jeyakanthan, J. / Kavyashree, M. / Sekar, K. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of Enoyl-CoA hydrates (gk_1992) from Geobacillus Kaustophilus HTA426
Authors: Kanaujia, S.P. / Jeyakanthan, J. / Kavyashree, M. / Sekar, K. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S.
History
DepositionMay 1, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase
C: Enoyl-CoA hydratase
D: Enoyl-CoA hydratase
E: Enoyl-CoA hydratase
F: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,27014
Polymers179,5096
Non-polymers7618
Water19,7801098
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34120 Å2
ΔGint-157 kcal/mol
Surface area49750 Å2
MethodPISA
2
A: Enoyl-CoA hydratase
C: Enoyl-CoA hydratase
E: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0296
Polymers89,7543
Non-polymers2743
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-63 kcal/mol
Surface area30000 Å2
MethodPISA
3
B: Enoyl-CoA hydratase
D: Enoyl-CoA hydratase
F: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2418
Polymers89,7543
Non-polymers4875
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12210 Å2
ΔGint-55 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.201, 137.345, 79.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Enoyl-CoA hydratase /


Mass: 29918.135 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta834(DE3) / References: UniProt: Q5KYF9, enoyl-CoA hydratase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1098 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 40% PEG 400, 100mM imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97915, 0.97973, 0.90000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 9, 2006 / Details: RH COATED BENT-CYRINDRICAL MIRROR
RadiationMonochromator: SI-1 1 1 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979731
30.91
ReflectionResolution: 2.15→50 Å / Num. all: 149368 / Num. obs: 149368 / % possible obs: 100 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.096
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.291 / Num. unique all: 7898 / Rsym value: 0.296 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.16→39.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 590396.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WEW USED FOR PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2940 2 %RANDOM
Rwork0.176 ---
obs0.176 149368 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.8456 Å2 / ksol: 0.351477 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2--4.96 Å20 Å2
3----4.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.16→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12363 0 50 1098 13511
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.15→2.25 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.277 320 2 %
Rwork0.234 15648 -
obs--81.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligand.paramligand.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION5water_rep.paramwater_protin.top

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