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- PDB-6tow: Structure of E70A mutant of Rex8A from Paenibacillus barcinonensi... -

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Basic information

Entry
Database: PDB / ID: 6tow
TitleStructure of E70A mutant of Rex8A from Paenibacillus barcinonensis complexed with xylotetraose.
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: 2.05 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 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 30, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
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)90,4504
Polymers89,3572
Non-polymers1,0932
Water5,603311
1
A: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2252
Polymers44,6781
Non-polymers5461
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)45,2252
Polymers44,6781
Non-polymers5461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.573, 84.573, 274.597
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
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: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 6 - 385 / Label seq-ID: 6 - 385

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

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Components

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


Mass: 44678.430 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: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a212h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.27 Å3/Da / Density % sol: 62.44 % / Description: Bar
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 3350, 0.2M Potassium thiocyanate, 0.1M Bis-Tris propane pH 7.5. Microseeding. Co-crystallization with 50-100mM xylotetraose.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2017 / Details: KB Mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.05→43.98 Å / Num. obs: 72614 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Net I/σ(I): 12.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4419 / CC1/2: 0.904 / Rpim(I) all: 0.264 / Rrim(I) all: 0.695 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimless7.0.029data scaling
MOLREP7.0.029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SRD

6srd


Resolution: 2.05→43.98 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.941 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.171
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 3464 4.8 %RANDOM
Rwork0.2361 ---
obs0.2374 69094 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.69 Å2 / Biso mean: 31.885 Å2 / Biso min: 17.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.53 Å20 Å2
2--1.07 Å20 Å2
3----3.46 Å2
Refinement stepCycle: final / Resolution: 2.05→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6248 0 74 311 6633
Biso mean--45.61 36.36 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136554
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175507
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.6728917
X-RAY DIFFRACTIONr_angle_other_deg1.3771.612779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59921.611422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50415951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4371551
X-RAY DIFFRACTIONr_chiral_restr0.0790.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021607
Refine LS restraints NCS

Ens-ID: 1 / Number: 13925 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 278 -
Rwork0.274 5005 -
all-5283 -
obs--99.92 %

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