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- PDB-6srd: Structure of Rex8A from Paenibacillus barcinonensis complexed wit... -

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Basic information

Entry
Database: PDB / ID: 6srd
TitleStructure 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: 1.93 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 5, 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)89,7158
Polymers89,0462
Non-polymers6696
Water10,917606
1
A: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8584
Polymers44,5231
Non-polymers3343
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)44,8584
Polymers44,5231
Non-polymers3343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.566, 59.153, 79.534
Angle α, β, γ (deg.)87.830, 77.980, 74.330
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / 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: _ / 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: 44523.223 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: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 52.61 % / Description: Bar
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 23% PEG 6K, 0.1 M Tris pH 8.0, 0.2 M NaCl, 0.01 M Hexammine cobalt (III) chrloride. Soaking experiment in the precipitant solution supplemented with 50 mM xylose. Cryoprotectan solution ...Details: 23% PEG 6K, 0.1 M Tris pH 8.0, 0.2 M NaCl, 0.01 M Hexammine cobalt (III) chrloride. Soaking experiment in the precipitant solution supplemented with 50 mM xylose. Cryoprotectan solution consisting of mother liquor plus 25% (v/v) glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.04191 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015 / Details: KB Mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04191 Å / Relative weight: 1
ReflectionResolution: 1.93→48.63 Å / Num. obs: 64154 / % possible obs: 96.4 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.078 / Rrim(I) all: 0.148 / Net I/σ(I): 7.2
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / Num. unique obs: 4213 / CC1/2: 0.663 / Rpim(I) all: 0.489 / Rrim(I) all: 0.879 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless7.0.042data scaling
MOLREP7.0.042phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WU4

1wu4


Resolution: 1.93→48.63 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.819 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 3260 5.1 %RANDOM
Rwork0.1889 ---
obs0.1909 60880 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.4 Å2 / Biso mean: 16.208 Å2 / Biso min: 5.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å21.09 Å20.4 Å2
2--0.31 Å2-0.74 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.93→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6226 0 44 613 6883
Biso mean--23.48 28.37 -
Num. residues----754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136480
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175454
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.668798
X-RAY DIFFRACTIONr_angle_other_deg1.3621.58112646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95121.706422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64115952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6321550
X-RAY DIFFRACTIONr_chiral_restr0.0760.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021594
Refine LS restraints NCS

Ens-ID: 1 / Number: 13932 / 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: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 236 -
Rwork0.246 4412 -
all-4648 -
obs--93.26 %

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