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- PDB-7l1z: Unlocking the structural features for the exo-xylobiosidase activ... -

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Basic information

Entry
Database: PDB / ID: 7l1z
TitleUnlocking the structural features for the exo-xylobiosidase activity of an unusual GH11 member identified in a compost-derived consortium - NT-truncated form
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: 2.05 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 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation_author / database_2
Item: _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,41023
Polymers74,6593
Non-polymers1,75120
Water9,116506
1
A: Exo-B-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5258
Polymers24,8861
Non-polymers6387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exo-B-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4918
Polymers24,8861
Non-polymers6047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Exo-B-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3957
Polymers24,8861
Non-polymers5086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.562, 149.686, 79.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21B-487-

HOH

31B-558-

HOH

41C-510-

HOH

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Components

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


Mass: 24886.350 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Metatranscriptome / Source: (gene. exp.) unidentified (others) / Plasmid: pETM11/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium cacodylate trihydrate pH 6.5 and 30% (w/v) PEG 8000

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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: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.05→49.62 Å / Num. obs: 50051 / % possible obs: 99.98 % / Redundancy: 13.1 % / CC1/2: 0.997 / Rpim(I) all: 0.061 / Rrim(I) all: 0.2226 / Net I/σ(I): 11.7
Reflection shellResolution: 2.05→2.12 Å / Num. unique obs: 4942 / CC1/2: 0.641 / Rpim(I) all: 0.4272 / Rrim(I) all: 1.499

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3794refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L1W

7l1w


Resolution: 2.05→49.62 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 2411 4.82 %
Rwork0.1859 47640 -
obs0.1879 50051 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.45 Å2 / Biso mean: 31.716 Å2 / Biso min: 12.76 Å2
Refinement stepCycle: final / Resolution: 2.05→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 95 506 5899
Biso mean--53.33 35.16 -
Num. residues----663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.05-2.090.29091370.249927892926
2.09-2.140.2721410.243727542895
2.14-2.190.27161300.228327652895
2.19-2.240.24461490.213227722921
2.24-2.30.26911350.208927632898
2.3-2.370.25121420.209627972939
2.37-2.450.27191180.207127972915
2.45-2.530.25441630.216527602923
2.53-2.630.2791380.21527752913
2.63-2.750.21661220.197328132935
2.75-2.90.24831350.202127942929
2.9-3.080.2691570.201127952952
3.08-3.320.22991310.173828272958
3.32-3.650.18851570.151527932950
3.65-4.180.17091470.147728292976
4.18-5.270.18631680.136928373005
5.27-49.620.23891410.213329803121
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9734-1.02571.05480.8066-0.44381.4278-0.10820.08440.0140.00670.0305-0.2084-0.12370.077-0.01560.12530.0014-0.03370.15340.01230.2046-14.4579-29.02254.2406
22.7253-0.17460.20310.9298-0.05860.96180.00310.27340.0165-0.1649-0.0240.0614-0.0010.0229-0.00090.1445-0.00350.00940.1178-0.00830.122313.5088-52.05991.6936
30.7774-0.6379-0.67241.67051.08681.27780.09730.02920.08920.0133-0.0521-0.0825-0.2279-0.0323-0.04780.2034-0.0076-0.01770.1525-0.00070.086426.576-4.1101-17.7614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 27:247)A27 - 247
2X-RAY DIFFRACTION2(chain B and resseq 27:247)B27 - 247
3X-RAY DIFFRACTION3(chain C and resseq 27:247)C27 - 247

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