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- PDB-7dfn: Crystal structure of glycoside hydrolase family 11 beta-xylanase ... -

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Basic information

Entry
Database: PDB / ID: 7dfn
TitleCrystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with alpha-L-arabinofuranosyl xylotetraose
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / glycoside hydrolase family 11
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Twin arginine translocation (Tat) signal profile. ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesStreptomyces olivaceoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFujimoto, Z. / Kishine, N. / Kaneko, S.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2021
Title: Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86.
Authors: Fujimoto, Z. / Kishine, N. / Teramoto, K. / Tsutsui, S. / Kaneko, S.
History
DepositionNov 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 10, 2021Group: 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 1.3Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
B: Endo-1,4-beta-xylanase
C: Endo-1,4-beta-xylanase
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,30067
Polymers90,1494
Non-polymers4,15063
Water8,125451
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,87721
Polymers22,5371
Non-polymers1,34020
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-16 kcal/mol
Surface area7950 Å2
MethodPISA
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,78318
Polymers22,5371
Non-polymers1,24617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area7920 Å2
MethodPISA
3
C: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,71216
Polymers22,5371
Non-polymers1,17515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area7960 Å2
MethodPISA
4
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,92712
Polymers22,5371
Non-polymers39011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.233, 134.233, 72.235
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-310-

CL

21D-457-

HOH

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Components

#1: Protein
Endo-1,4-beta-xylanase


Mass: 22537.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: GB LC578783
Source: (gene. exp.) Streptomyces olivaceoviridis (bacteria)
Strain: E-86 / Gene: gxyn1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A7G1MBT0*PLUS, endo-1,4-beta-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.: 3 / Source method: obtained synthetically
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: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.08 Å3/Da / Density % sol: 40.98 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 2.9 M sodium chloride, 0.1 M sodium citrate buffer pH 5.4

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 50743 / % possible obs: 99.8 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.257 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 48052

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DFM

7dfm


Resolution: 2→49.217 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.599 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.159
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 2660 5.245 %ramdom
Rwork0.1649 48052 --
all0.167 ---
obs-50712 99.768 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.681 Å20.34 Å20 Å2
2--0.681 Å20 Å2
3----2.209 Å2
Refinement stepCycle: LAST / Resolution: 2→49.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5965 0 198 451 6614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126317
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185107
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.6878623
X-RAY DIFFRACTIONr_angle_other_deg1.3641.611870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5425767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.822.073328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09615840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0181531
X-RAY DIFFRACTIONr_chiral_restr0.0610.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027199
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021526
X-RAY DIFFRACTIONr_nbd_refined0.1770.2982
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.24833
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23047
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22967
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2424
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0160.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1040.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.219
X-RAY DIFFRACTIONr_nbd_other0.1990.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.225
X-RAY DIFFRACTIONr_mcbond_it1.5272.2353080
X-RAY DIFFRACTIONr_mcbond_other1.5232.2343079
X-RAY DIFFRACTIONr_mcangle_it2.1733.3443843
X-RAY DIFFRACTIONr_mcangle_other2.1733.3443844
X-RAY DIFFRACTIONr_scbond_it2.0412.4613236
X-RAY DIFFRACTIONr_scbond_other2.042.4613236
X-RAY DIFFRACTIONr_scangle_it3.1113.6274778
X-RAY DIFFRACTIONr_scangle_other3.1113.6274779
X-RAY DIFFRACTIONr_lrange_it4.3325.647206
X-RAY DIFFRACTIONr_lrange_other4.30725.6147195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2741810.2493465X-RAY DIFFRACTION97.5649
2.052-2.1080.2931680.2313433X-RAY DIFFRACTION99.7507
2.108-2.1690.271680.2183367X-RAY DIFFRACTION100
2.169-2.2360.2441760.1913274X-RAY DIFFRACTION100
2.236-2.3090.2451630.1883162X-RAY DIFFRACTION100
2.309-2.390.231690.1783029X-RAY DIFFRACTION100
2.39-2.4810.2641530.1912959X-RAY DIFFRACTION99.9679
2.481-2.5820.2331630.182848X-RAY DIFFRACTION99.8673
2.582-2.6970.2321760.1842695X-RAY DIFFRACTION100
2.697-2.8280.2351730.1892572X-RAY DIFFRACTION99.7094
2.828-2.9810.2011220.172510X-RAY DIFFRACTION100
2.981-3.1620.2221460.1692328X-RAY DIFFRACTION100
3.162-3.380.1891130.1462232X-RAY DIFFRACTION100
3.38-3.650.1551100.1322081X-RAY DIFFRACTION100
3.65-3.9980.1781170.1211898X-RAY DIFFRACTION100
3.998-4.470.1421060.1031733X-RAY DIFFRACTION100
4.47-5.160.152990.1131522X-RAY DIFFRACTION100
5.16-6.3160.182690.1511304X-RAY DIFFRACTION100
6.316-8.920.227590.1681041X-RAY DIFFRACTION100
8.92-49.2170.202290.195599X-RAY DIFFRACTION99.2101

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