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- PDB-5yae: Ferulic acid esterase from Streptomyces cinnamoneus at 2.4 A reso... -

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Basic information

Entry
Database: PDB / ID: 5yae
TitleFerulic acid esterase from Streptomyces cinnamoneus at 2.4 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 / SAD / Resolution: 2.4 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
DepositionAug 31, 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 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)37,4716
Polymers37,0651
Non-polymers4065
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-11 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.270, 71.290, 87.720
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: ammonium sulfate, sodium cacodylate trihydrate (pH 6.5), PEG 8000, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7 Å / Relative weight: 1
ReflectionResolution: 2.34→55.32 Å / Num. obs: 14597 / % possible obs: 93.9 % / Redundancy: 30.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 42.9
Reflection shellResolution: 2.4→2.47 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 10.6 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→55.32 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.497 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.566 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22026 629 4.8 %RANDOM
Rwork0.1805 ---
obs0.18248 12536 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.458 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.4→55.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 23 94 2710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192685
X-RAY DIFFRACTIONr_bond_other_d0.0020.022572
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9783662
X-RAY DIFFRACTIONr_angle_other_deg0.94235903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64421.593113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72715410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3111533
X-RAY DIFFRACTIONr_chiral_restr0.070.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02608
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_it0.8221.5761363
X-RAY DIFFRACTIONr_mcbond_other0.8221.5731360
X-RAY DIFFRACTIONr_mcangle_it1.4832.3561700
X-RAY DIFFRACTIONr_mcangle_other1.4832.3561701
X-RAY DIFFRACTIONr_scbond_it0.9311.7391322
X-RAY DIFFRACTIONr_scbond_other0.9311.7411323
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6282.5571962
X-RAY DIFFRACTIONr_long_range_B_refined2.97418.3122868
X-RAY DIFFRACTIONr_long_range_B_other2.97218.3132863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 42 -
Rwork0.214 820 -
obs--87.69 %

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