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- PDB-2jeq: Family 5 xyloglucanase from Paenibacillus pabuli in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2jeq
TitleFamily 5 xyloglucanase from Paenibacillus pabuli in complex with ligand
ComponentsXYLOGLUCANASE
KeywordsHYDROLASE / FAMILY 5 / XYLOGLUCANASE / PLANT CELL WALL
Function / homology
Function and homology information


xyloglucan-specific endo-beta-1,4-glucanase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesPAENIBACILLUS PABULI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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. ...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. / 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. / Borchert, T.V. / Wilson, K.S. ...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. / 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_special_symmetry / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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.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
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 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XYLOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0632
Polymers43,9701
Non-polymers1,0931
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)85.066, 89.160, 38.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2056-

HOH

21A-2159-

HOH

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Components

#1: Protein XYLOGLUCANASE


Mass: 43969.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PAENIBACILLUS PABULI (bacteria) / Strain: DSM13330 / Production host: BACILLUS SUBTILIS (bacteria)
References: UniProt: H9KVH3*PLUS, xyloglucan-specific endo-beta-1,4-glucanase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D- ...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)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1092.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-1-1-1-2-2-3/a4-b1_b4-c1_b6-f1_c4-d1_c6-e1_f2-g1WURCSPDB2Glycan 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]{[(2+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 36 RESIDUES CANNOT BE OBSERVED. THE FIRST 32 OF THESE ARE LIKELY TO BE A SIGNAL PEPTIDE ...THE FIRST 36 RESIDUES CANNOT BE OBSERVED. THE FIRST 32 OF THESE ARE LIKELY TO BE A SIGNAL PEPTIDE CLEAVED DURING EXPRESSION OF THE PROTEIN.

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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: 1.8 Å3/Da / Density % sol: 32.1 %
Crystal growpH: 8.5 / Details: 25% PEG 3350, 0.2 M MGCL2, 0.1 M TRIS, PH 8.5

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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: 1.95→50 Å / Num. obs: 22170 / % possible obs: 98.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 91.7

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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 2JEP

2jep


Resolution: 1.94→61.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.629 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1117 5.1 %RANDOM
Rwork0.182 ---
obs0.186 20757 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---1.5 Å20 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.94→61.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 74 247 3164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9394248
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07725.597159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92515472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.452159
X-RAY DIFFRACTIONr_chiral_restr0.0970.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022411
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21532
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22131
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.290
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7911.51867
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2722957
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.94731437
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8614.51274
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: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.261 76
Rwork0.253 1391

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