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

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Basic information

Entry
Database: PDB / ID: 6trh
TitleStructure of E70A mutant of Rex8A from Paenibacillus barcinonensis complexed with 3(3)-alpha-L-arabinofuranosyl-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: 1.86 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 18, 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 / Refinement description / 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 / refine_hist / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _refine_hist.d_res_high / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
C: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
D: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,4288
Polymers178,7144
Non-polymers2,7144
Water3,459192
1
A: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3572
Polymers44,6781
Non-polymers6791
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)45,3572
Polymers44,6781
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3572
Polymers44,6781
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Reducing-end xylose-releasing exo-oligoxylanase Rex8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3572
Polymers44,6781
Non-polymers6791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.295, 82.720, 465.317
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA6 - 3846 - 384
21LYSLYSBB6 - 3846 - 384
12GLYGLYAA5 - 3845 - 384
22GLYGLYCC5 - 3845 - 384
13LYSLYSAA6 - 3846 - 384
23LYSLYSDD6 - 3846 - 384
14LYSLYSBB6 - 3846 - 384
24LYSLYSCC6 - 3846 - 384
15LYSLYSBB6 - 3856 - 385
25LYSLYSDD6 - 3856 - 385
16LYSLYSCC6 - 3846 - 384
26LYSLYSDD6 - 3846 - 384

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 44678.430 Da / Num. of mol.: 4
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
alpha-L-arabinofuranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D- ...alpha-L-arabinofuranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 678.589 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-3[DXylpb1-4]DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a212h-1b_1-5][a211h-1a_1-4]/1-1-1-2-1/a4-b1_b4-c1_c3-d1_c4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(3+1)][a-L-Araf]{}[(4+1)][b-D-Xylp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.29 Å3/Da / Density % sol: 46.21 % / Description: Bar
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Potassium thiocyanate, 0.1M Bis Tris propane pH 7.5. Microseeding. Co-crystallization: 5 mM 3(3)-alpha-L-arabinofuranosyl-xylotetraose. Cryoprotectant: 25% Glycerol.

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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: Oct 20, 2019 / 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.52
11-K, -H, -L20.48
ReflectionResolution: 1.85→46.62 Å / Num. obs: 129847 / % possible obs: 97.2 % / Redundancy: 7.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.052 / Rrim(I) all: 0.162 / Net I/σ(I): 8
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1 / Num. unique obs: 5330 / CC1/2: 0.568 / Rpim(I) all: 0.377 / Rrim(I) all: 0.768 / % possible all: 80.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDS0.84data reduction
Aimless7.0.077data scaling
MOLREP7.0.077phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SRD

6srd


Resolution: 1.86→46.62 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.914 / SU B: 2.931 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 6472 5 %RANDOM
Rwork0.2385 ---
obs0.2398 123280 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.88 Å2 / Biso mean: 33.218 Å2 / Biso min: 16.47 Å2
Baniso -1Baniso -2Baniso -3
1--8.51 Å20 Å20 Å2
2---6.95 Å20 Å2
3---15.46 Å2
Refinement stepCycle: final / Resolution: 1.86→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12535 0 184 194 12913
Biso mean--21.56 33.16 -
Num. residues----1526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01313188
X-RAY DIFFRACTIONr_bond_other_d0.0040.01811077
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.67717949
X-RAY DIFFRACTIONr_angle_other_deg1.241.60625720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6651528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42321.631846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.792151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.27315102
X-RAY DIFFRACTIONr_chiral_restr0.0810.21601
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215071
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023219
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A139470.05
12B139470.05
21A139290.05
22C139290.05
31A139820.04
32D139820.04
41B139640.05
42C139640.05
51B140130.05
52D140130.05
61C140320.04
62D140320.04
LS refinement shellResolution: 1.86→1.899 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 323 -
Rwork0.261 6260 -
all-6583 -
obs--66.03 %

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