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- PDB-7b6b: The carbohydrate binding module family 48 (CBM48) and carboxy-ter... -

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Basic information

Entry
Database: PDB / ID: 7b6b
TitleThe carbohydrate binding module family 48 (CBM48) and carboxy-terminal carbohydrate esterase family 1 (CE1) domains of the multidomain esterase DmCE1B from Dysgonomonas mossii in complex with methyl ferulate
ComponentsCarbohydrate Esterase family 1 protein with an N-terminal carbohydrate binding module family 48
KeywordsHYDROLASE / carbohydrate esterase / CE1 / CBM48 / carbohydrate binding module / CBM / CE / PUL / lignin / xylan / ferulate / ferouyl esterase
Function / homologyEsterase-like / Putative esterase / Immunoglobulin E-set / Alpha/Beta hydrolase fold / Immunoglobulin-like fold / Trans-methylferulate / Esterase
Function and homology information
Biological speciesDysgonomonas mossii DSM 22836 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsMazurkewich, S. / Kmezik, C. / Branden, G. / Larsbrink, J.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-03931 Sweden
Novo Nordisk FoundationNNF17OC0027648 Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases.
Authors: Kmezik, C. / Mazurkewich, S. / Meents, T. / McKee, L.S. / Idstrom, A. / Armeni, M. / Savolainen, O. / Branden, G. / Larsbrink, J.
History
DepositionDec 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate Esterase family 1 protein with an N-terminal carbohydrate binding module family 48
B: Carbohydrate Esterase family 1 protein with an N-terminal carbohydrate binding module family 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3598
Polymers86,7212
Non-polymers6386
Water13,025723
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-22 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.258, 50.511, 90.148
Angle α, β, γ (deg.)90.000, 100.137, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Carbohydrate Esterase family 1 protein with an N-terminal carbohydrate binding module family 48


Mass: 43360.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dysgonomonas mossii DSM 22836 (bacteria)
Gene: HMPREF9456_02279 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8X1N1
#2: Chemical ChemComp-SZQ / Trans-methylferulate / methyl (~{E})-3-(3-methoxy-4-oxidanyl-phenyl)prop-2-enoate


Mass: 208.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.89 Å3/Da / Density % sol: 35.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Tris pH 8, 25% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.408→43.9 Å / Num. obs: 123374 / % possible obs: 98.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.15 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 16.49
Reflection shellResolution: 1.408→1.459 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.35 / Num. unique obs: 10521 / CC1/2: 0.823 / CC star: 0.95 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B5V

7b5v


Resolution: 1.41→43.9 Å / SU ML: 0.1251 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9857
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1789 9253 7.5 %
Rwork0.1607 114115 -
obs0.1621 123368 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.96 Å2
Refinement stepCycle: LAST / Resolution: 1.41→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 43 723 6256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00865882
X-RAY DIFFRACTIONf_angle_d1.02617987
X-RAY DIFFRACTIONf_chiral_restr0.0902828
X-RAY DIFFRACTIONf_plane_restr0.00661055
X-RAY DIFFRACTIONf_dihedral_angle_d19.52532157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.420.26112470.23743046X-RAY DIFFRACTION80.36
1.42-1.440.26722670.23573292X-RAY DIFFRACTION84.8
1.44-1.460.2342750.22143393X-RAY DIFFRACTION88.3
1.46-1.480.24292950.21063634X-RAY DIFFRACTION93.93
1.48-1.50.2343110.21023833X-RAY DIFFRACTION99.98
1.5-1.520.24543100.19413830X-RAY DIFFRACTION99.98
1.52-1.540.22323170.18653919X-RAY DIFFRACTION100
1.54-1.560.20413120.17813835X-RAY DIFFRACTION99.98
1.56-1.590.18623110.17953834X-RAY DIFFRACTION99.98
1.59-1.610.20543120.17463857X-RAY DIFFRACTION100
1.61-1.640.20843120.17093852X-RAY DIFFRACTION99.98
1.64-1.670.20793130.16693860X-RAY DIFFRACTION100
1.67-1.70.17883130.16273853X-RAY DIFFRACTION100
1.7-1.740.18123140.16363876X-RAY DIFFRACTION99.98
1.74-1.770.19163100.16693819X-RAY DIFFRACTION99.98
1.77-1.820.1943150.16733886X-RAY DIFFRACTION99.95
1.82-1.860.19013140.16993865X-RAY DIFFRACTION99.98
1.86-1.910.20933120.17273856X-RAY DIFFRACTION99.98
1.91-1.970.18873130.16363849X-RAY DIFFRACTION99.95
1.97-2.030.18483150.16333901X-RAY DIFFRACTION99.98
2.03-2.10.17593150.1613879X-RAY DIFFRACTION99.93
2.1-2.190.18393120.16183853X-RAY DIFFRACTION99.93
2.19-2.290.18683160.16413897X-RAY DIFFRACTION99.91
2.29-2.410.18343130.1683857X-RAY DIFFRACTION99.9
2.41-2.560.18523150.17293885X-RAY DIFFRACTION99.88
2.56-2.760.17313140.1663880X-RAY DIFFRACTION99.9
2.76-3.030.183160.16233891X-RAY DIFFRACTION99.69
3.03-3.470.1623180.14943917X-RAY DIFFRACTION99.83
3.47-4.370.13923180.12843924X-RAY DIFFRACTION99.91
4.37-43.90.16093280.14624042X-RAY DIFFRACTION99.75

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