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- PDB-5bv9: The Structure of Bacillus pumilus GH48 in complex with cellobiose -

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Basic information

Entry
Database: PDB / ID: 5bv9
TitleThe Structure of Bacillus pumilus GH48 in complex with cellobiose
ComponentsCellulose 1,4-beta-cellobiosidase
KeywordsHYDROLASE / GH48 / cellulase / cellobiose
Function / homology
Function and homology information


cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Beta Complex ...Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-cellobiose / ACETATE ION / MALONATE ION / Glycoside hydrolase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Proteins / Year: 2016
Title: Strategies to reduce end-product inhibition in family 48 glycoside hydrolases.
Authors: Chen, M. / Bu, L. / Alahuhta, M. / Brunecky, R. / Xu, Q. / Lunin, V.V. / Brady, J.W. / Crowley, M.F. / Himmel, M.E. / Bomble, Y.J.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulose 1,4-beta-cellobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,41819
Polymers79,9351
Non-polymers1,48318
Water17,114950
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.291, 97.291, 218.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1462-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Cellulose 1,4-beta-cellobiosidase /


Mass: 79934.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Strain: SAFR-032 / Gene: celB, BPUM_1559 / Production host: Escherichia coli (E. coli)
References: UniProt: A8FDC4, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 967 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 950 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2.4 M Sodium malonate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 79431 / % possible obs: 99.8 % / Redundancy: 8.72 % / Rsym value: 0.1713 / Net I/σ(I): 9.58
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 3.93 % / Mean I/σ(I) obs: 2.03 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G9G

1g9g


Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.749 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20747 3950 5 %RANDOM
Rwork0.16132 ---
obs0.1636 74971 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å2-0 Å2
2--0.58 Å2-0 Å2
3----1.15 Å2
Refinement stepCycle: 1 / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5581 0 94 950 6625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025972
X-RAY DIFFRACTIONr_bond_other_d0.0030.025180
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.9298135
X-RAY DIFFRACTIONr_angle_other_deg1.108311959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33824.62303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0515866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3531522
X-RAY DIFFRACTIONr_chiral_restr0.1260.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217021
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021489
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5341.5242878
X-RAY DIFFRACTIONr_mcbond_other1.5121.5162871
X-RAY DIFFRACTIONr_mcangle_it2.2762.2713611
X-RAY DIFFRACTIONr_mcangle_other2.2782.2733612
X-RAY DIFFRACTIONr_scbond_it2.4041.7523094
X-RAY DIFFRACTIONr_scbond_other2.4031.7523094
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7282.5384525
X-RAY DIFFRACTIONr_long_range_B_refined6.7514.198368
X-RAY DIFFRACTIONr_long_range_B_other5.72113.3277790
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 282 -
Rwork0.299 5469 -
obs--99.43 %

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