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- PDB-6sgf: Molecular insight into a new low affinity xylan binding module CB... -

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Basic information

Entry
Database: PDB / ID: 6sgf
TitleMolecular insight into a new low affinity xylan binding module CBM86, from the xylanolytic gut symbiont Roseburia intestinalis.
ComponentsBeta-xylanase
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding module / Xylanase / Xylan / Roseburia inteternalis.
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process / carbohydrate binding
Similarity search - Function
Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Invasin/intimin cell-adhesion fragments / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 ...Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Invasin/intimin cell-adhesion fragments / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding-like domain superfamily / Fibronectin type III superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
4beta-beta-xylotriose / : / beta-D-xylopyranose / Beta-xylanase
Similarity search - Component
Biological speciesRoseburia intestinalis L1-82 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.756 Å
AuthorsEjby, M. / Abou Hachem, M. / Leth, M.L. / Guskov, A. / Slotboom, D.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research4002-00297B Denmark
CitationJournal: Febs J. / Year: 2020
Title: Molecular insight into a new low-affinity xylan binding module from the xylanolytic gut symbiont Roseburia intestinalis.
Authors: Leth, M.L. / Ejby, M. / Madland, E. / Kitaoku, Y. / Slotboom, D.J. / Guskov, A. / Aachmann, F.L. / Abou Hachem, M.
History
DepositionAug 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
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 / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase
C: Beta-xylanase
D: Beta-xylanase
E: Beta-xylanase
F: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,75031
Polymers90,0466
Non-polymers4,70525
Water12,232679
1
A: Beta-xylanase
hetero molecules

B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,79513
Polymers30,0152
Non-polymers1,77911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3910 Å2
ΔGint-82 kcal/mol
Surface area12210 Å2
MethodPISA
2
C: Beta-xylanase
D: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,66411
Polymers30,0152
Non-polymers1,6499
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-61 kcal/mol
Surface area12470 Å2
MethodPISA
3
E: Beta-xylanase
F: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2927
Polymers30,0152
Non-polymers1,2765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-50 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.870, 141.870, 60.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 28 through 114 or resid 116 through 156))
21(chain B and (resid 28 through 114 or resid 116 through 156))
31(chain C and (resid 28 through 114 or resid 116 through 156))
41(chain D and (resid 28 through 114 or resid 116 through 156))
51(chain E and (resid 28 through 114 or resid 116 through 156))
61(chain F and (resid 28 through 114 or resid 116 through 156))
12chain G
22chain J
32chain K
42chain M
52chain O

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 28 through 114 or resid 116 through 156))A28 - 114
121(chain A and (resid 28 through 114 or resid 116 through 156))A116 - 156
211(chain B and (resid 28 through 114 or resid 116 through 156))B28 - 114
221(chain B and (resid 28 through 114 or resid 116 through 156))B116 - 156
311(chain C and (resid 28 through 114 or resid 116 through 156))C28 - 114
321(chain C and (resid 28 through 114 or resid 116 through 156))C116 - 156
411(chain D and (resid 28 through 114 or resid 116 through 156))D28 - 114
421(chain D and (resid 28 through 114 or resid 116 through 156))D116 - 156
511(chain E and (resid 28 through 114 or resid 116 through 156))E28 - 114
521(chain E and (resid 28 through 114 or resid 116 through 156))E116 - 156
611(chain F and (resid 28 through 114 or resid 116 through 156))F28 - 114
621(chain F and (resid 28 through 114 or resid 116 through 156))F116 - 156
112chain GG1 - 4
212chain JJ1 - 4
312chain KK1 - 4
412chain MM1 - 4
512chain OO1 - 4

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Beta-xylanase


Mass: 15007.638 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseburia intestinalis L1-82 (bacteria)
Gene: ROSINTL182_06494 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7G9B5, endo-1,4-beta-xylanase

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Sugars , 3 types, 7 molecules

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


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 414.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligosaccharide / References: 4beta-beta-xylotriose
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
[][<C5O3>]{[(1+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: 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.: 5 / Source method: obtained synthetically
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
#4: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 697 molecules

#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: Cd
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystal grew for 2 days at 5 C with a 1:1 ratio of the protein (18 mg/mL in 10 mM MES pH 6.5,150 mM NaCl and 1mM xylohexaose) and reservoir solution (0.2 M Cadmium chloride hemi(pentahydrate) ...Details: Crystal grew for 2 days at 5 C with a 1:1 ratio of the protein (18 mg/mL in 10 mM MES pH 6.5,150 mM NaCl and 1mM xylohexaose) and reservoir solution (0.2 M Cadmium chloride hemi(pentahydrate), 0.1 M Sodium acetate pH 4.8 and PEG 400 35 % v/v).
Temp details: 5C cold room

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.756→46.438 Å / Num. obs: 127404 / % possible obs: 97 % / Redundancy: 5.8 % / Biso Wilson estimate: 21.84 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.032 / Rrim(I) all: 0.08 / Rsym value: 0.062 / Net I/av σ(I): 7 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.76-1.852.30.5281.41829580600.4230.7110.5282.280.7
1.85-1.963.70.3132.23499794680.210.4110.3134.699.1
1.96-2.16.20.2173.15576489600.1020.2570.2178.9100
2.1-2.277.10.1554.35930483720.0680.1810.15512.3100
2.27-2.486.80.1066.35288677210.0480.1270.10615100
2.48-2.786.80.0798.24722969950.0380.0990.07917.9100
2.78-3.2170.0599.64317961740.0280.0750.05923.4100
3.21-3.936.40.04511.33336052160.0230.0590.04529.499.8
3.93-5.556.90.03912.12836440850.0190.0510.03935.199.9
5.55-46.3646.30.03512.51451422990.020.0530.03530.899.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.756→46.438 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.16 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 4734 3.72 %
Rwork0.1789 122670 -
obs0.1806 127404 93.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.82 Å2 / Biso mean: 28.6569 Å2 / Biso min: 5.4 Å2
Refinement stepCycle: final / Resolution: 1.756→46.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5954 0 443 679 7076
Biso mean--34.36 33.51 -
Num. residues----787
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2268X-RAY DIFFRACTION6.507TORSIONAL
12B2268X-RAY DIFFRACTION6.507TORSIONAL
13C2268X-RAY DIFFRACTION6.507TORSIONAL
14D2268X-RAY DIFFRACTION6.507TORSIONAL
15E2268X-RAY DIFFRACTION6.507TORSIONAL
16F2268X-RAY DIFFRACTION6.507TORSIONAL
21C20X-RAY DIFFRACTION6.507TORSIONAL
22B20X-RAY DIFFRACTION6.507TORSIONAL
23E20X-RAY DIFFRACTION6.507TORSIONAL
24F20X-RAY DIFFRACTION6.507TORSIONAL
25D20X-RAY DIFFRACTION6.507TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7561-1.77613590520
1.7761-1.7970.407910.384234854
1.797-1.81890.37611360.3521355882
1.8189-1.84190.3622163381688
1.8419-1.86620.4073151402992
1.8662-1.89170.2754158415594
1.8917-1.91880.2679157413096
1.9188-1.94740.2502163427597
1.9474-1.97780.2499168429098
1.9778-2.01030.2275167432598
2.0103-2.04490.2637168431199
2.0449-2.08210.16671660.1635430299
2.0821-2.12220.21511660.16534380100
2.1222-2.16550.21881640.1603432399
2.1655-2.21260.27261720.15384372100
2.2126-2.2640.20231580.1495433999
2.264-2.32060.17971720.14194367100
2.3206-2.38340.18691580.14814310100
2.3834-2.45350.21491700.1622439499
2.4535-2.53270.2433170435799
2.5327-2.62320.24921524352100
2.6232-2.72820.22121824304100
2.7282-2.85240.25111744381100
2.8524-3.00270.2051664352100
3.0027-3.19080.2002176432699
3.1908-3.43710.2172178432499
3.4371-3.78290.16921660.1523432699
3.7829-4.32990.18781640.15164361100
4.3299-5.45390.19631640.15214343100
5.4539-100.2917159431599

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