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- PDB-2jen: Family 12 xyloglucanase from Bacillus licheniformis in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2jen
TitleFamily 12 xyloglucanase from Bacillus licheniformis in complex with ligand
ComponentsENDO-BETA-1,4-GLUCANASE
KeywordsHYDROLASE / PLANT CELL WALL / GLYCOSIDASE / XYLOGLUCANASE / FAMILY 12
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Cellulase 12A
Similarity search - Component
Biological speciesBACILLUS LICHENIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K.S. ...Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K.S. / Borchert, T.V. / Wilson, K.S. / Brumer, H. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Characterization and Three-Dimensional Structures of Two Distinct Bacterial Xyloglucanases from Families Gh5 and Gh12.
Authors: Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K.S. / Borchert, T.V. / Wilson, K. ...Authors: Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K.S. / Borchert, T.V. / Wilson, K.S. / Brumer, H. / Davies, G.J.
History
DepositionJan 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_chiral / 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_alt_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_alt_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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-BETA-1,4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0338
Polymers29,0351
Non-polymers1,9987
Water6,503361
1
A: ENDO-BETA-1,4-GLUCANASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)186,19848
Polymers174,2116
Non-polymers11,98742
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_345-x-4/3,-x+y-2/3,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)114.629, 114.629, 110.302
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ENDO-BETA-1,4-GLUCANASE / XYLOGLUCANASE


Mass: 29035.178 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS LICHENIFORMIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q7X4S4, cellulase, xyloglucan-specific endo-beta-1,4-glucanase

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 930.808 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1a_1-5][a2122h-1b_1-5][a212h-1a_1-5]/1-1-2-2-3-3/a4-b1_b4-c1_b6-f1_c4-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][b-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]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-xylopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]alpha-D-glucopyranose


Type: oligosaccharide / Mass: 606.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpa1-4[DXylpa1-6]DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a212h-1a_1-5]/1-1-2-2/a4-b1_a6-d1_b6-c1WURCSPDB2Glycan 1.1.0
[][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 , 4 types, 366 molecules

#4: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 155 TO ALA

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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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.5
Details: 1.6M AMMONIUM SULPHATE, 10% DIOXANE, 0.1M MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 4, 2003 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 54792 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.3
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0011refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JEM

2jem


Resolution: 1.4→74.54 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.273 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.141 2779 5.1 %RANDOM
Rwork0.115 ---
obs0.116 52009 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.4→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 132 361 2339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212213
X-RAY DIFFRACTIONr_bond_other_d0.0030.021422
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9643072
X-RAY DIFFRACTIONr_angle_other_deg1.04833476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.875276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87324.84295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0115313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.916154
X-RAY DIFFRACTIONr_chiral_restr0.1770.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022383
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02446
X-RAY DIFFRACTIONr_nbd_refined0.1870.2327
X-RAY DIFFRACTIONr_nbd_other0.1910.21462
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21074
X-RAY DIFFRACTIONr_nbtor_other0.0910.21110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5741.51292
X-RAY DIFFRACTIONr_mcbond_other0.7261.5507
X-RAY DIFFRACTIONr_mcangle_it2.11222037
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.09331145
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0584.51015
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.50634434
X-RAY DIFFRACTIONr_sphericity_free7.9973361
X-RAY DIFFRACTIONr_sphericity_bonded3.58933543
LS refinement shellResolution: 1.4→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 192 -
Rwork0.134 3694 -
obs--97.22 %

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