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- PDB-6ehn: Structural insight into a promiscuous CE15 esterase from the mari... -

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Basic information

Entry
Database: PDB / ID: 6ehn
TitleStructural insight into a promiscuous CE15 esterase from the marine bacterial metagenome
ComponentsCarbohydrate esterase MZ0003
KeywordsHYDROLASE / esterase / protein structure
Function / homologyHydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / polysaccharide catabolic process / Alpha/Beta hydrolase fold / periplasmic space / Carbohydrate esterase MZ0003
Function and homology information
Biological speciesUnknown prokaryotic organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.9 Å
AuthorsHelland, R. / De Santi, C. / Gani, O. / Williamson, A.K.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway247732 Norway
Research Council of Norway Norway
CitationJournal: Sci Rep / Year: 2017
Title: Structural insight into a CE15 esterase from the marine bacterial metagenome.
Authors: De Santi, C. / Gani, O.A. / Helland, R. / Williamson, A.
History
DepositionSep 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Carbohydrate esterase MZ0003
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9822
Polymers44,8901
Non-polymers921
Water5,675315
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint1 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.212, 110.212, 78.666
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Carbohydrate esterase MZ0003


Mass: 44889.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Unknown prokaryotic organism (environmental samples)
Gene: MZ0003 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K2VM55, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, 24% NaCitrate, pH 6, 0.1 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91840, 1.28202
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
21.282021
ReflectionResolution: 1.9→47 Å / Num. obs: 43689 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 25.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.031 / Rrim(I) all: 0.074 / Net I/av σ(I): 16.4 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.945.60.59327740.6460.270.652100
2.1-2.1611.70.93924070.40998.5

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
Aimless0.5.8data scaling
PHASERphasing
SOLVEphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.9→47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.427 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.125
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2077 4.8 %RANDOM
Rwork0.1832 ---
obs0.1852 41585 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.43 Å2 / Biso mean: 33.169 Å2 / Biso min: 7.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.11 Å2-0 Å2
2---0.21 Å20 Å2
3---0.69 Å2
Refinement stepCycle: final / Resolution: 1.9→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 6 315 3411
Biso mean--31.86 38.65 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193220
X-RAY DIFFRACTIONr_bond_other_d0.0020.022957
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.9334378
X-RAY DIFFRACTIONr_angle_other_deg1.14936779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.6265403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54323.4150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06715500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4761521
X-RAY DIFFRACTIONr_chiral_restr0.1480.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213718
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02785
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 143 -
Rwork0.328 3024 -
all-3167 -
obs--99.97 %

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