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- PDB-3wyd: C-terminal esterase domain of LC-Est1 -

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Basic information

Entry
Database: PDB / ID: 3wyd
TitleC-terminal esterase domain of LC-Est1
ComponentsLC-Est1C
KeywordsHYDROLASE / Leaf-branch compost / Metagenome / Alpha/beta hydrolase fold / Esterase
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity
Similarity search - Function
: / Cutinase / PET hydrolase-like / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.53 Å
AuthorsOkano, H. / Hong, X. / Angkawidjaja, C. / Kanaya, S.
CitationJournal: Protein Sci. / Year: 2015
Title: Structural and biochemical characterization of a metagenome-derived esterase with a long N-terminal extension.
Authors: Okano, H. / Hong, X. / Kanaya, E. / Angkawidjaja, C. / Kanaya, S.
History
DepositionAug 26, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LC-Est1C
B: LC-Est1C


Theoretical massNumber of molelcules
Total (without water)50,2712
Polymers50,2712
Non-polymers00
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-13 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.861, 55.446, 156.275
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 LC-Est1C


Mass: 25135.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured organism (environmental samples)
Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A6YVN5*PLUS, carboxylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KM406409 FOR THE SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium chloride, 0.1M BIS-TRIS, 25% PEG3,350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU20.978769, 0.979101, 0.994813
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDMay 19, 2014
RAYONIX MX225HE2CCDJul 18, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rotated-inclined double crystalSINGLE WAVELENGTHMx-ray1
2Rotated-inclined double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.9787691
30.9791011
40.9948131
ReflectionResolution: 1.53→78.14 Å / Num. obs: 60179 / % possible obs: 98.5 % / Observed criterion σ(I): 5 / Redundancy: 6.5 % / Rmerge(I) obs: 0.181 / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.53→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.281 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22481 3030 5.1 %RANDOM
Rwork0.19069 ---
obs0.1924 56727 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.156 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.53→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2992 0 0 451 3443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223073
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9414162
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66922.867143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99915479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1091523
X-RAY DIFFRACTIONr_chiral_restr0.1160.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212393
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6491.51901
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.56323053
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.79831172
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7074.51109
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.571 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 233 -
Rwork0.246 4164 -
obs--99.82 %

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