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- PDB-6tpp: Structure of E70A mutant of Rex8A from Paenibacillus barcinonensis. -

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Basic information

Entry
Database: PDB / ID: 6tpp
TitleStructure of E70A 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: 2.64 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
DepositionDec 13, 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)89,1796
Polymers88,9302
Non-polymers2484
Water3,981221
1
A: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5893
Polymers44,4651
Non-polymers1242
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)44,5893
Polymers44,4651
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.697, 58.735, 79.320
Angle α, β, γ (deg.)87.320, 78.190, 73.490
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: 44465.191 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.63 Å3/Da / Density % sol: 53.25 % / Description: Bar
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 6000, 0.1M HEPES pH 7, 0.2M magnesium chloride, 6% glycerol, 0.01M Hexammine cobalt(III) chloride. Microseeding. Cryoprotectant: 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: May 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: 2.64→77.63 Å / Num. obs: 24307 / % possible obs: 94.4 % / Redundancy: 3 % / CC1/2: 0.971 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.109 / Rrim(I) all: 0.198 / Net I/σ(I): 5.4
Reflection shellResolution: 2.64→2.77 Å / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3296 / CC1/2: 0.563 / Rpim(I) all: 0.595 / Rrim(I) all: 0.824 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless7.0.077data scaling
MOLREP7.0.077phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SRD

6srd


Resolution: 2.64→77.63 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.895 / SU B: 14.392 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.342
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 1157 4.8 %RANDOM
Rwork0.1902 ---
obs0.1924 23147 94.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97 Å2 / Biso mean: 26.787 Å2 / Biso min: 7.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å21.16 Å20.51 Å2
2--0.63 Å2-0.75 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 2.64→77.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6218 0 16 227 6461
Biso mean--33.57 25.21 -
Num. residues----754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136444
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175434
X-RAY DIFFRACTIONr_angle_refined_deg1.451.6578748
X-RAY DIFFRACTIONr_angle_other_deg1.3291.57712590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4335752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0121.667420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85715948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2661550
X-RAY DIFFRACTIONr_chiral_restr0.0710.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021594
Refine LS restraints NCS

Ens-ID: 1 / Number: 13528 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.64→2.709 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 94 -
Rwork0.283 1716 -
all-1810 -
obs--94.62 %

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