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Basic information

Entry
Database: PDB / ID: 2ebs
TitleCrystal Structure Anaalysis of Oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH) D465N Mutant Complexed with a Xyloglucan Heptasaccharide
ComponentsOligoxyloglucan reducing end-specific cellobiohydrolase
KeywordsHYDROLASE / BETA-PROPELLER / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


oligoxyloglucan reducing-end-specific cellobiohydrolase / oligoxyloglucan reducing-end-specific cellobiohydrolase activity / xyloglucan metabolic process / cellulose catabolic process
Similarity search - Function
BNR-Asp box repeat / : / BNR repeat / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Oligoxyloglucan reducing end-specific cellobiohydrolase
Similarity search - Component
Biological speciesGeotrichum sp. M128 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYaoi, K. / Kondo, H. / Hiyoshi, A. / Noro, N. / Sugimoto, H. / Miyazaki, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The Structural Basis for the Exo-mode of Action in GH74 Oligoxyloglucan Reducing End-specific Cellobiohydrolase.
Authors: Yaoi, K. / Kondo, H. / Hiyoshi, A. / Noro, N. / Sugimoto, H. / Tsuda, S. / Mitsuishi, Y. / Miyazaki, K.
#1: Journal: Structure / Year: 2004
Title: Tandem repeat of a seven-bladed beta-propeller domain in oligoxyloglucan reducing-end-specific cellobiohydrolase
Authors: Yaoi, K. / Kondo, H. / Noro, N. / Suzuki, M. / Tsuda, S. / Mitsuishi, Y.
History
DepositionFeb 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2007Group: 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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_struct_assembly_gen.asym_id_list / _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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oligoxyloglucan reducing end-specific cellobiohydrolase
B: Oligoxyloglucan reducing end-specific cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0734
Polymers169,9472
Non-polymers2,1262
Water19,4201078
1
A: Oligoxyloglucan reducing end-specific cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0372
Polymers84,9741
Non-polymers1,0631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oligoxyloglucan reducing end-specific cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0372
Polymers84,9741
Non-polymers1,0631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.970, 147.515, 212.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Oligoxyloglucan reducing end-specific cellobiohydrolase / OXG-RCBH


Mass: 84973.742 Da / Num. of mol.: 2 / Fragment: residues 1-789 / Mutation: D465N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geotrichum sp. M128 (yeast) / Plasmid: pET29a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codonplus(de3)rp
References: UniProt: Q8J0D2, oligoxyloglucan reducing-end-specific cellobiohydrolase
#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)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1062.923 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-1-2-2-2/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-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]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1078 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 100mM MES pH5.2-5.3, 5-6% (w/v) PEG 3000, 40% (w/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2004
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 72255 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 6.1 / % possible all: 82.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SQJ

1sqj


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.525 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.347 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21925 3638 5.1 %RANDOM
Rwork0.1585 ---
obs0.16164 68375 95.09 %-
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: 22.134 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--1.38 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11709 0 144 1078 12931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02212228
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.94216724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22751535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95824.267532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.277151679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4751552
X-RAY DIFFRACTIONr_chiral_restr0.0980.21780
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029564
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.26110
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.28202
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.21238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6011.57757
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.057212233
X-RAY DIFFRACTIONr_scbond_it1.68535257
X-RAY DIFFRACTIONr_scangle_it2.6564.54491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 236 -
Rwork0.192 4232 -
obs--81.62 %

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