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- PDB-7l1w: Unlocking the structural features for the exo-xylobiosidase activ... -

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Basic information

Entry
Database: PDB / ID: 7l1w
TitleUnlocking the structural features for the exo-xylobiosidase activity of an unusual GH11 member identified in a compost-derived consortium
ComponentsExo-B-1,4-beta-xylanase
KeywordsHYDROLASE / glycoside hydrolase family 11 / GH11 Exo-B-1 / 4-xylobiosidase
Function / homologyGlycoside hydrolase family 11/12, catalytic domain / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsKadowaki, M.A.S. / Polikarpov, I. / Briganti, L. / Evangelista, D.E.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)15/13684-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303988/2016-9 Brazil
CitationJournal: Biotechnol.Bioeng. / Year: 2021
Title: Unlocking the structural features for the xylobiohydrolase activity of an unusual GH11 member identified in a compost-derived consortium.
Authors: Kadowaki, M.A.S. / Briganti, L. / Evangelista, D.E. / Echevarria-Poza, A. / Tryfona, T. / Pellegrini, V.O.A. / Nakayama, D.G. / Dupree, P. / Polikarpov, I.
History
DepositionDec 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exo-B-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8772
Polymers27,6811
Non-polymers1951
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.950, 96.950, 40.899
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21A-596-

HOH

31A-606-

HOH

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Components

#1: Protein Exo-B-1,4-beta-xylanase


Mass: 27681.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Metatranscriptome / Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH 6.5 and 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.71→27.99 Å / Num. obs: 23891 / % possible obs: 99.92 % / Redundancy: 18.1 % / Biso Wilson estimate: 20.11 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.0269 / Rrim(I) all: 0.1163 / Net I/σ(I): 19.92
Reflection shellResolution: 1.71→1.77 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 2358 / CC1/2: 0.668 / Rpim(I) all: 0.5463 / Rrim(I) all: 1.956

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Processing

Software
NameVersionClassification
PHENIXPhenix.Refinerefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VQJ

5vqj


Resolution: 1.71→27.99 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1921 -4.72 %
Rwork0.1593 --
obs0.1609 23889 99.93 %
Displacement parametersBiso mean: 22.73 Å2
Refinement stepCycle: LAST / Resolution: 1.71→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 12 242 2203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582042
X-RAY DIFFRACTIONf_angle_d0.85592788
X-RAY DIFFRACTIONf_chiral_restr0.0588273
X-RAY DIFFRACTIONf_plane_restr0.0058363
X-RAY DIFFRACTIONf_dihedral_angle_d17.4238714

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