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- PDB-2w87: Xyl-CBM35 in complex with glucuronic acid containing disaccharide. -

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Basic information

Entry
Database: PDB / ID: 2w87
TitleXyl-CBM35 in complex with glucuronic acid containing disaccharide.
ComponentsESTERASE D
KeywordsHYDROLASE / PLANT CELL WALL DEGRADATION / CARBOHYDRATE PROTEIN BINDING / XYLAN / CMB35 / GLUCURONIC ACID
Function / homology
Function and homology information


feruloyl esterase activity / xylan catabolic process / polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region / metal ion binding
Similarity search - Function
Feruloyl esterase B/C/D / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate binding module (family 6) / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM6 (carbohydrate binding type-6) domain profile. ...Feruloyl esterase B/C/D / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate binding module (family 6) / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / CBM2/CBM3, carbohydrate-binding domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-glucopyranuronic acid / Unknown ligand / Esterase D
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMontainer, C. / Bueren, A.L.v. / Dumon, C. / Flint, J.E. / Correia, M.A. / Prates, J.A. / Firbank, S.J. / Lewis, R.J. / Grondin, G.G. / Ghinet, M.G. ...Montainer, C. / Bueren, A.L.v. / Dumon, C. / Flint, J.E. / Correia, M.A. / Prates, J.A. / Firbank, S.J. / Lewis, R.J. / Grondin, G.G. / Ghinet, M.G. / Gloster, T.M. / Herve, C. / Knox, J.P. / Talbot, B.G. / Turkenburg, J.P. / Kerovuo, J. / Brzezinski, R. / Fontes, C.M.G.A. / Davies, G.J. / Boraston, A.B. / Gilbert, H.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Evidence that Family 35 Carbohydrate Binding Modules Display Conserved Specificity But Divergent Function.
Authors: Montanier, C. / Van Bueren, A.L. / Dumon, C. / Flint, J.E. / Correia, M.A. / Prates, J.A. / Firbank, S.J. / Lewis, R.J. / Grondin, G.G. / Ghinet, M.G. / Gloster, T.M. / Herve, C. / Knox, J.P. ...Authors: Montanier, C. / Van Bueren, A.L. / Dumon, C. / Flint, J.E. / Correia, M.A. / Prates, J.A. / Firbank, S.J. / Lewis, R.J. / Grondin, G.G. / Ghinet, M.G. / Gloster, T.M. / Herve, C. / Knox, J.P. / Talbot, B.G. / Turkenburg, J.P. / Kerovuo, J. / Brzezinski, R. / Fontes, C.M.G.A. / Davies, G.J. / Boraston, A.B. / Gilbert, H.J.
History
DepositionJan 14, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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: ESTERASE D
B: ESTERASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,85110
Polymers28,3032
Non-polymers5498
Water5,477304
1
A: ESTERASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4265
Polymers14,1511
Non-polymers2744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ESTERASE D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4265
Polymers14,1511
Non-polymers2744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)27.850, 45.450, 48.910
Angle α, β, γ (deg.)71.79, 89.74, 81.28
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ESTERASE D / XYL-CBM35


Mass: 14151.377 Da / Num. of mol.: 2 / Fragment: RESIDUES 160-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(STAR)DE3
References: UniProt: Q51815, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-GCU / alpha-D-glucopyranuronic acid / alpha-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsGLUCURONIC ACID CONTAINING DISACCHARIDE (GCU): SUGAR NOT CHARACTERISED. GLUCURONIC ACID CLEAR IN ...GLUCURONIC ACID CONTAINING DISACCHARIDE (GCU): SUGAR NOT CHARACTERISED. GLUCURONIC ACID CLEAR IN DENSITY, BUT IDENTITY OF SECOND SUGAR UNKNOWN.

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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 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 6.9 / Details: 20% PEG 3350, 0.4M THIOCYANATE PH 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06
DetectorType: ADSC CCD / Detector: CCD
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.58→24 Å / Num. obs: 30820 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.7
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.4 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W46

2w46


Resolution: 1.6→24.15 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.711 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1372 5 %RANDOM
Rwork0.143 ---
obs0.145 26229 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-1.26 Å20.3 Å2
2--1.25 Å2-0.44 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 44 304 2316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212103
X-RAY DIFFRACTIONr_bond_other_d0.0020.021253
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9372905
X-RAY DIFFRACTIONr_angle_other_deg0.8113.0053060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5225302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22125.90988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.53815284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.806159
X-RAY DIFFRACTIONr_chiral_restr0.0780.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_nbd_refined0.2190.2374
X-RAY DIFFRACTIONr_nbd_other0.2130.21379
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21084
X-RAY DIFFRACTIONr_nbtor_other0.0840.21225
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1760.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0871.51401
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66422232
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3363773
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3444.5661
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 82
Rwork0.167 1738

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