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- PDB-5yal: Ferulic acid esterase from Streptomyces cinnamoneus at 1.5 A reso... -

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Basic information

Entry
Database: PDB / ID: 5yal
TitleFerulic acid esterase from Streptomyces cinnamoneus at 1.5 A resolution
ComponentsEsterase
KeywordsHYDROLASE / Ferulic acid esterase / Catalytic triad / Serine protease
Function / homologyPlatelet-activating factor acetylhydrolase, isoform II / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid catabolic process / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha/Beta hydrolase fold / ACETATE ION / Esterase
Function and homology information
Biological speciesStreptomyces cinnamoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTamura, H. / Uraji, M. / Mizohata, E. / Ogawa, K. / Inoue, T. / Hatanaka, T.
CitationJournal: Appl. Environ. Microbiol. / Year: 2018
Title: Loop of Streptomyces Feruloyl Esterase Plays an Important Role in the Enzyme's Catalyzing the Release of Ferulic Acid from Biomass.
Authors: Uraji, M. / Tamura, H. / Mizohata, E. / Arima, J. / Wan, K. / Ogawa, K. / Inoue, T. / Hatanaka, T.
History
DepositionSep 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Nov 22, 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2394
Polymers37,0651
Non-polymers1743
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-10 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.900, 70.850, 87.170
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 Esterase


Mass: 37065.191 Da / Num. of mol.: 1 / Fragment: UNP residues 42-383 / Mutation: P8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cinnamoneus (bacteria) / Gene: estA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4UW33, feruloyl esterase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 8000, sodium acetate trihydrate, sodium cacodylate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→42.4 Å / Num. obs: 53162 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.7
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YAE

5yae


Resolution: 1.5→42.39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.269 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20094 2658 5 %RANDOM
Rwork0.17992 ---
obs0.18096 50503 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.749 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.5→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 11 223 2844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192708
X-RAY DIFFRACTIONr_bond_other_d0.0020.022608
X-RAY DIFFRACTIONr_angle_refined_deg1.181.9743694
X-RAY DIFFRACTIONr_angle_other_deg0.89735989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88521.638116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.77215418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1581534
X-RAY DIFFRACTIONr_chiral_restr0.0640.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02618
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_it0.6011.6921374
X-RAY DIFFRACTIONr_mcbond_other0.6021.6911372
X-RAY DIFFRACTIONr_mcangle_it1.0942.5341716
X-RAY DIFFRACTIONr_mcangle_other1.0942.5341717
X-RAY DIFFRACTIONr_scbond_it0.6191.7871334
X-RAY DIFFRACTIONr_scbond_other0.6191.7871334
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0652.6461976
X-RAY DIFFRACTIONr_long_range_B_refined3.59813.9643149
X-RAY DIFFRACTIONr_long_range_B_other3.14613.623052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 193 -
Rwork0.243 3676 -
obs--99.97 %

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