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- PDB-6sud: Structure of L320A mutant of Rex8A from Paenibacillus barcinonens... -

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Basic information

Entry
Database: PDB / ID: 6sud
TitleStructure of L320A mutant of Rex8A from Paenibacillus barcinonensis complexed with xylose.
ComponentsReducing-end xylose-releasing exo-oligoxylanase Rex8A
KeywordsHYDROLASE / Xylan / Exo-oligoxylanase / Xylanases / Xylooligosaccharides / Xylooligomers / Xylose / Hydrolysis / Polysaccharides / Glycan / Glycan degradation / Xylan degradation / Glycosidase / Carbohydrate metabolism.
Function / homology
Function and homology information


oligosaccharide reducing-end xylanase / oligosaccharide reducing-end xylanase activity / xylan catabolic process
Similarity search - Function
Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
beta-D-xylopyranose / Reducing-end xylose-releasing exo-oligoxylanase Rex8A
Similarity search - Component
Biological speciesPaenibacillus barcinonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsJimenez-Ortega, E. / Ramirez-Escudero, M. / Sanz-Aparicio, J.
CitationJournal: Febs J. / Year: 2020
Title: Structural analysis of the reducing-end xylose-releasing exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 deciphers its molecular specificity.
Authors: Jimenez-Ortega, E. / Valenzuela, S. / Ramirez-Escudero, M. / Pastor, F.J. / Sanz-Aparicio, J.
History
DepositionSep 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 30, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
B: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,52621
Polymers88,9622
Non-polymers1,56419
Water10,755597
1
A: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,24610
Polymers44,4811
Non-polymers7659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,28011
Polymers44,4811
Non-polymers79910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.514, 59.172, 79.412
Angle α, β, γ (deg.)87.830, 78.350, 74.610
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 6 - 382 / Label seq-ID: 6 - 382

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Reducing-end xylose-releasing exo-oligoxylanase Rex8A / Rex


Mass: 44481.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus barcinonensis (bacteria) / Gene: rex8A, DFQ00_11062 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0S2UQQ5, oligosaccharide reducing-end xylanase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.6 Å3/Da / Density % sol: 52.68 % / Description: Bar
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 22% PEG 6000, 0.1 M HEPES pH 7, 0.2 M MgCl2, 6% glycerol, 0.01 M Hexammine cobalt (III) chloride. Microseeding. Soaking: 50 mM xylose, 100 mM arabinose. Cryoprotectant solution: mother ...Details: 22% PEG 6000, 0.1 M HEPES pH 7, 0.2 M MgCl2, 6% glycerol, 0.01 M Hexammine cobalt (III) chloride. Microseeding. Soaking: 50 mM xylose, 100 mM arabinose. Cryoprotectant solution: mother liquor plus 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2016 / Details: KB Mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.74→57.11 Å / Num. obs: 87761 / % possible obs: 96.6 % / Redundancy: 3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.067 / Rrim(I) all: 0.119 / Net I/σ(I): 7.1
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4448 / CC1/2: 0.787 / Rpim(I) all: 0.423 / Rrim(I) all: 0.759 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless7.0.012data scaling
MOLREP7.0.012phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WU4

1wu4


Resolution: 1.74→57.11 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.886 / SU B: 3.294 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.143
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 4370 5 %RANDOM
Rwork0.2421 ---
obs0.2438 83378 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 47.94 Å2 / Biso mean: 14.37 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å21.1 Å20.15 Å2
2--0.12 Å2-0.4 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.74→57.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 102 601 6923
Biso mean--23.31 24.82 -
Num. residues----754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136558
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175543
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.6668884
X-RAY DIFFRACTIONr_angle_other_deg1.441.58412854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5625760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38621.745424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07515958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3961550
X-RAY DIFFRACTIONr_chiral_restr0.0770.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021602
Refine LS restraints NCS

Ens-ID: 1 / Number: 13846 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 300 -
Rwork0.284 6082 -
all-6382 -
obs--94.98 %

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