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- PDB-4w8b: Crystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4-gl... -

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Basic information

Entry
Database: PDB / ID: 4w8b
TitleCrystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal metagenomic library, in complex with XXLG
ComponentsExo-xyloglucanase
KeywordsHYDROLASE / glycoside hydrolase / cell wall degrading enzyme / GH5 family
Function / homology
Function and homology information


beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.15 Å
AuthorsSantos, C.R. / Cordeiro, R.L. / Wong, D.W.S. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/13309-0, 2014/07135-1 Brazil
CitationJournal: Biochemistry / Year: 2015
Title: Structural Basis for Xyloglucan Specificity and alpha-d-Xylp(1 6)-d-Glcp Recognition at the -1 Subsite within the GH5 Family.
Authors: Dos Santos, C.R. / Cordeiro, R.L. / Wong, D.W. / Murakami, M.T.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 2.0Nov 22, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / software / struct_conn / struct_keywords / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_label_asym_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_keywords.text / _struct_site_gen.label_asym_id
Revision 2.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Jan 1, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 27, 2023Group: 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: Exo-xyloglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1488
Polymers42,6821
Non-polymers2,4667
Water12,214678
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.632, 120.632, 59.004
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Exo-xyloglucanase


Mass: 42681.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cow's rumen
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: D2XML9

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1225.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1a_1-5][a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-2-2-2-3-3-3-4/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1_g2-h1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 768.667 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-2-2/a4-b1_b4-c1_b6-e1_c6-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 683 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: ammonium sulfate, sodium citrate, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 165780 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 11.637 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.056 / Χ2: 0.94 / Net I/σ(I): 26.38 / Num. measured all: 1377786
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allRmerge(I) obsMean I/σ(I) obs
1.15-1.220.95616192027913239720.29485.9
1.22-1.30.98222518326246255190.24497.20.2310.14
1.3-1.410.98921154824406238890.18897.90.17712.98
1.41-1.540.99519422122497221220.12898.30.1218.42
1.54-1.720.99716711820398195870.089960.08325.54
1.72-1.990.99914227217972173810.05996.70.05536.61
1.99-2.440.99911700015274149180.04197.70.03851.22
2.44-3.44110078711850117490.0399.10.02867.31
3.44157737665166430.02299.90.0281.55

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementResolution: 1.15→39.49 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.502 / SU ML: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.005 / ESU R Free: 0.005 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1224 8301 5 %RANDOM
Rwork0.1031 157480 --
obs0.1041 157480 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 176.06 Å2 / Biso mean: 9.959 Å2 / Biso min: 3.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0 Å2-0 Å2
2---1.28 Å2-0 Å2
3---2.56 Å2
Refinement stepCycle: final / Resolution: 1.15→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 164 678 3854
Biso mean--17.57 26.53 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0193292
X-RAY DIFFRACTIONr_bond_other_d0.0020.022913
X-RAY DIFFRACTIONr_angle_refined_deg2.1921.9674501
X-RAY DIFFRACTIONr_angle_other_deg1.54136707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67725.217161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34915480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.619159
X-RAY DIFFRACTIONr_chiral_restr0.1660.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023667
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02776
X-RAY DIFFRACTIONr_mcbond_it1.2770.6491543
X-RAY DIFFRACTIONr_mcbond_other1.2740.6491542
X-RAY DIFFRACTIONr_mcangle_it1.60.9821927
X-RAY DIFFRACTIONr_rigid_bond_restr7.75236177
X-RAY DIFFRACTIONr_sphericity_free45.4275102
X-RAY DIFFRACTIONr_sphericity_bonded13.74656669
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 496 -
Rwork0.159 9206 -
all-9702 -
obs--75.99 %

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