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- PDB-3l3s: Crystal structure of an enoyl-CoA hydrotase/isomerase family prot... -

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Basic information

Entry
Database: PDB / ID: 3l3s
TitleCrystal structure of an enoyl-CoA hydrotase/isomerase family protein from Silicibacter pomeroyi
ComponentsEnoyl-CoA hydratase/isomerase family protein
KeywordsISOMERASE / crotonase superfamily / dimer of trimers / PSI-2 / NYSGXRC / 11252f / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


hydro-lyase activity
Similarity search - Function
: / Helix Hairpins - #2460 / 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 / Helix Hairpins / Alpha-Beta Complex / Orthogonal Bundle ...: / Helix Hairpins - #2460 / 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 / Helix Hairpins / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Enoyl-CoA hydratase/isomerase family protein
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsEswaramoorthy, S. / Silberstein, M. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an enoyl-CoA hydrotase/isomerase family protein from Silicibacter pomeroyi
Authors: Eswaramoorthy, S. / Silberstein, M. / Burley, S.K. / Swaminathan, S.
History
DepositionDec 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 6, 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
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
C: Enoyl-CoA hydratase/isomerase family protein
D: Enoyl-CoA hydratase/isomerase family protein
E: Enoyl-CoA hydratase/isomerase family protein
F: Enoyl-CoA hydratase/isomerase family protein
G: Enoyl-CoA hydratase/isomerase family protein
H: Enoyl-CoA hydratase/isomerase family protein
I: Enoyl-CoA hydratase/isomerase family protein
J: Enoyl-CoA hydratase/isomerase family protein
K: Enoyl-CoA hydratase/isomerase family protein
L: Enoyl-CoA hydratase/isomerase family protein


Theoretical massNumber of molelcules
Total (without water)342,73812
Polymers342,73812
Non-polymers00
Water2,414134
1
A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
C: Enoyl-CoA hydratase/isomerase family protein


Theoretical massNumber of molelcules
Total (without water)85,6853
Polymers85,6853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-73 kcal/mol
Surface area25650 Å2
MethodPISA
2
D: Enoyl-CoA hydratase/isomerase family protein
E: Enoyl-CoA hydratase/isomerase family protein
F: Enoyl-CoA hydratase/isomerase family protein


Theoretical massNumber of molelcules
Total (without water)85,6853
Polymers85,6853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-75 kcal/mol
Surface area25300 Å2
MethodPISA
3
G: Enoyl-CoA hydratase/isomerase family protein
H: Enoyl-CoA hydratase/isomerase family protein
I: Enoyl-CoA hydratase/isomerase family protein


Theoretical massNumber of molelcules
Total (without water)85,6853
Polymers85,6853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-75 kcal/mol
Surface area25530 Å2
MethodPISA
4
J: Enoyl-CoA hydratase/isomerase family protein
K: Enoyl-CoA hydratase/isomerase family protein
L: Enoyl-CoA hydratase/isomerase family protein


Theoretical massNumber of molelcules
Total (without water)85,6853
Polymers85,6853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-77 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.403, 124.285, 146.999
Angle α, β, γ (deg.)90.00, 102.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enoyl-CoA hydratase/isomerase family protein


Mass: 28561.521 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Gene: SPO2339 / Plasmid: BC - pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon_RIL / References: UniProt: Q5LQZ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Lithium sulfate; 0.1M HEPES pH 7.5; 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 130351 / Num. obs: 130351 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.9
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.776 / Num. unique all: 12687 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VX2

2vx2


Resolution: 2.32→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 5005 -RANDOM
Rwork0.263 ---
all0.291 124154 --
obs0.291 124154 92.3 %-
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.84 Å20 Å2-0.59 Å2
2--12.58 Å20 Å2
3----7.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.32→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20515 0 0 134 20649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_deg1.76
LS refinement shellResolution: 2.32→2.4 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.383 635 -
Rwork0.353 --
obs-15817 70.8 %

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