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

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Basic information

Entry
Database: PDB / ID: 7dfo
TitleCrystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with 4-O-methyl-alpha-D-glucuronopyranosyl 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
E: Endo-1,4-beta-xylanase
F: Endo-1,4-beta-xylanase
G: Endo-1,4-beta-xylanase
H: Endo-1,4-beta-xylanase
I: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,67773
Polymers202,8369
Non-polymers5,84164
Water15,277848
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1528
Polymers22,5371
Non-polymers6157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3685
Polymers22,5371
Non-polymers8314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3789
Polymers22,5371
Non-polymers8408
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,80710
Polymers22,5371
Non-polymers2699
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1528
Polymers22,5371
Non-polymers6157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3685
Polymers22,5371
Non-polymers8314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5087
Polymers22,5371
Non-polymers9716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6795
Polymers22,5371
Non-polymers1424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,26616
Polymers22,5371
Non-polymers72915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.709, 142.709, 72.454
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 9 molecules ABCDEFGHI

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


Mass: 22537.367 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: GB LC578783
Source: (gene. exp.) Streptomyces olivaceoviridis (bacteria)
Strain: E-86 / Gene: soxB / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A7G1MBT0*PLUS, endo-1,4-beta-xylanase

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Sugars , 4 types, 8 molecules

#2: Polysaccharide
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)- ...4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 736.625 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,5,4/[a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-1-1-2-1/a4-b1_b4-c1_c2-d1_c4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}[(4+1)][b-D-Xylp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)- ...4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 604.510 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-1-1-2/a4-b1_b4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 904 molecules

#6: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.43 % / Description: rod
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: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 110677 / % possible obs: 99.3 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 17.9
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 11151

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Processing

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

7dfm


Resolution: 2→47.061 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.858 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.19 / ESU R Free: 0.166
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2176 5434 4.911 %
Rwork0.1651 105212 -
all0.168 --
obs-110646 99.239 %
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: 30.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.856 Å20.428 Å20 Å2
2--0.856 Å20 Å2
3----2.776 Å2
Refinement stepCycle: LAST / Resolution: 2→47.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13486 0 328 848 14662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01214219
X-RAY DIFFRACTIONr_bond_other_d0.0010.01811524
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.68119401
X-RAY DIFFRACTIONr_angle_other_deg1.3651.59626778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.31651738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06722.158732
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.709151899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.471567
X-RAY DIFFRACTIONr_chiral_restr0.0590.21856
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023431
X-RAY DIFFRACTIONr_nbd_refined0.1850.22148
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.210443
X-RAY DIFFRACTIONr_nbtor_refined0.180.26776
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.26344
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2698
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0890.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2060.220
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.220
X-RAY DIFFRACTIONr_nbd_other0.2170.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0570.21
X-RAY DIFFRACTIONr_mcbond_it2.2563.2386973
X-RAY DIFFRACTIONr_mcbond_other2.2563.2386972
X-RAY DIFFRACTIONr_mcangle_it2.9784.8418701
X-RAY DIFFRACTIONr_mcangle_other2.9784.8418702
X-RAY DIFFRACTIONr_scbond_it2.8453.5217246
X-RAY DIFFRACTIONr_scbond_other2.8443.5217246
X-RAY DIFFRACTIONr_scangle_it4.1615.19810699
X-RAY DIFFRACTIONr_scangle_other4.1615.19910700
X-RAY DIFFRACTIONr_lrange_it5.28136.57615842
X-RAY DIFFRACTIONr_lrange_other5.2836.5615835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2724100.2337827X-RAY DIFFRACTION99.8545
2.052-2.1080.2584620.2117575X-RAY DIFFRACTION100
2.108-2.1690.2474080.2047383X-RAY DIFFRACTION100
2.169-2.2360.2583760.197260X-RAY DIFFRACTION99.9869
2.236-2.3090.2473570.186946X-RAY DIFFRACTION100
2.309-2.390.263380.186834X-RAY DIFFRACTION99.9582
2.39-2.4810.2343400.1726487X-RAY DIFFRACTION99.9854
2.481-2.5820.243760.186300X-RAY DIFFRACTION99.985
2.582-2.6970.2413290.1865957X-RAY DIFFRACTION99.9682
2.697-2.8280.242640.1835787X-RAY DIFFRACTION99.9339
2.828-2.9810.2752700.1845485X-RAY DIFFRACTION99.74
2.981-3.1620.2222580.1725168X-RAY DIFFRACTION99.5962
3.162-3.380.1952320.1634828X-RAY DIFFRACTION99.0603
3.38-3.6510.2012180.1494468X-RAY DIFFRACTION98.239
3.651-3.9990.1711580.1384135X-RAY DIFFRACTION97.1927
3.999-4.470.1742010.1193512X-RAY DIFFRACTION93.9524
4.47-5.160.1691540.133137X-RAY DIFFRACTION94.1092
5.16-6.3170.1961310.1482754X-RAY DIFFRACTION98.2295
6.317-8.9230.1841000.1522198X-RAY DIFFRACTION99.6963
8.923-47.0610.202520.181171X-RAY DIFFRACTION98.4702

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