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- PDB-4zrs: Crystal structure of a cloned feruloyl esterase from a soil metag... -

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Basic information

Entry
Database: PDB / ID: 4zrs
TitleCrystal structure of a cloned feruloyl esterase from a soil metagenomic library
ComponentsEsterase
KeywordsHYDROLASE / feruloyl esterase / metagenomic library
Function / homologyLipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / Esterase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXie, W. / Chen, R. / Cao, L. / Liu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Sciences Foundation of China31100579 China
Guangdong Innovative Research Team2011Y038 China
CitationJournal: J.Agric.Food Chem. / Year: 2015
Title: Enhancing the Thermostability of Feruloyl Esterase EstF27 by Directed Evolution and the Underlying Structural Basis
Authors: Cao, L.C. / Chen, R. / Xie, W. / Liu, Y.H.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0924
Polymers66,9082
Non-polymers1842
Water11,079615
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.156, 101.790, 69.822
Angle α, β, γ (deg.)90.00, 110.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999961, -0.008652, -0.001736), (-0.008653, -0.999963, -0.000424), (-0.001733, 0.000439, -0.999998)0.19362, 17.91032, 65.31759

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Components

#1: Protein Esterase / feruloyl esterase


Mass: 33453.750 Da / Num. of mol.: 2 / Mutation: T27I, S84L, V161I, H195L, G243C, A259V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E7DJY5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.2 M ammonium sulfate, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54056 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2→65.35 Å / Num. obs: 45906 / % possible obs: 99.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NSP

4nsp


Resolution: 2→65.35 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.541 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 2322 5.1 %RANDOM
Rwork0.15001 ---
obs0.15247 43584 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.2 Å2
2--0.03 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→65.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 12 615 5065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194563
X-RAY DIFFRACTIONr_bond_other_d0.0010.024261
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9576201
X-RAY DIFFRACTIONr_angle_other_deg2.42439781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1515582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68123.266199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47415678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8141530
X-RAY DIFFRACTIONr_chiral_restr0.1040.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215246
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021072
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_it1.5451.6482334
X-RAY DIFFRACTIONr_mcbond_other1.5441.6472333
X-RAY DIFFRACTIONr_mcangle_it2.2842.4592914
X-RAY DIFFRACTIONr_mcangle_other2.2832.462915
X-RAY DIFFRACTIONr_scbond_it2.6891.9162229
X-RAY DIFFRACTIONr_scbond_other2.6891.9162229
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1012.7583288
X-RAY DIFFRACTIONr_long_range_B_refined6.47115.3075826
X-RAY DIFFRACTIONr_long_range_B_other6.47115.3075826
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 184 -
Rwork0.222 3209 -
obs--99.97 %

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