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- PDB-6shy: Structure of L320A/H321S double mutant of Rex8A from Paenibacillu... -

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Basic information

Entry
Database: PDB / ID: 6shy
TitleStructure of L320A/H321S double mutant of Rex8A from Paenibacillus barcinonensis
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
Reducing-end xylose-releasing exo-oligoxylanase Rex8A
Similarity search - Component
Biological speciesPaenibacillus barcinonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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
DepositionAug 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: 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 1.2Jan 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

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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)89,97720
Polymers88,8602
Non-polymers1,11718
Water8,773487
1
A: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,05111
Polymers44,4301
Non-polymers62110
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)44,9279
Polymers44,4301
Non-polymers4978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.302, 58.580, 78.677
Angle α, β, γ (deg.)87.510, 78.080, 74.320
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: 44430.078 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


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.54 Å3/Da / Density % sol: 51.5 % / Description: Bar
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 6000, 0.1 M Tris pH 8.0, 0.2 M NaCl, 10% MPD, 0.01 M Hexammine cobalt(III) chloride. Microseeding.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2017 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.81→45.82 Å / Num. obs: 75674 / % possible obs: 96.2 % / Redundancy: 2.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.077 / Rrim(I) all: 0.136 / Net I/σ(I): 5.6
Reflection shellResolution: 1.81→1.85 Å / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2 / Num. unique obs: 4471 / CC1/2: 0.622 / Rpim(I) all: 0.463 / Rrim(I) all: 0.801 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless7.0.039data scaling
MOLREP7.0.039phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WU4

1wu4


Resolution: 1.81→45.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.779 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.118
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3752 5 %RANDOM
Rwork0.1761 ---
obs0.1776 71922 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.66 Å2 / Biso mean: 19.645 Å2 / Biso min: 10.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å21.08 Å20.02 Å2
2--0.24 Å2-0.65 Å2
3---0.58 Å2
Refinement stepCycle: final / Resolution: 1.81→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6212 0 72 487 6771
Biso mean--36.5 30.74 -
Num. residues----754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136501
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175502
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6618802
X-RAY DIFFRACTIONr_angle_other_deg1.561.57712747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2535758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74221.734421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28115951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5541550
X-RAY DIFFRACTIONr_chiral_restr0.0810.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027496
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021594
Refine LS restraints NCS

Ens-ID: 1 / Number: 13659 / 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: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 270 -
Rwork0.238 5238 -
all-5508 -
obs--94.77 %

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