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- PDB-6d5d: Structure of Caldicellulosiruptor danielii GH48 module of glycosi... -

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Basic information

Entry
Database: PDB / ID: 6d5d
TitleStructure of Caldicellulosiruptor danielii GH48 module of glycoside hydrolase WP_045175321
Componentsglycoside hydrolase WP_045175321
KeywordsHYDROLASE / GH48 / glycoside hydrolase
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 / Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase ...Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / 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 / Glycoside hydrolase WP_045175321
Similarity search - Component
Biological speciesCaldicellulosiruptor sp. Wai35.B1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: AIChE J. / Year: 2019
Title: Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species
Authors: Conway, J.M. / Crosby, J.R. / Hren, A.P. / Southerland, R.T. / Lee, L.L. / Lunin, V.V. / Alahuhta, P.M. / Himmel, M.E. / Bomble, Y.J. / Adams, M.W.W. / Kelly, R.M.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 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 / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / 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 / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _citation.country / _citation.journal_id_ISSN / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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

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Assembly

Deposited unit
A: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5184
Polymers73,7931
Non-polymers7253
Water14,538807
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-8 kcal/mol
Surface area21060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.014, 57.512, 105.957
Angle α, β, γ (deg.)90.00, 103.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1435-

HOH

21A-1481-

HOH

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Components

#1: Protein glycoside hydrolase WP_045175321


Mass: 73792.945 Da / Num. of mol.: 1 / Fragment: GH48 module
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor sp. Wai35.B1 (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: A0A4V8GZQ9*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M citric acid, pH 5-6, 20% 2-propanol, 0.05 M trisodium citrate, 14-25% PEG4000

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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: May 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 53369 / % possible obs: 99.2 % / Redundancy: 5.35 % / Rpim(I) all: 0.0613 / Net I/σ(I): 9.95
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.99 % / Mean I/σ(I) obs: 1.94 / Num. unique obs: 7332 / Rpim(I) all: 0.3521 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SAINTdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EL8

4el8


Resolution: 1.9→103.08 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.149 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23122 2577 4.8 %RANDOM
Rwork0.16268 ---
obs0.16598 50559 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.103 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-0.01 Å2
2--0.59 Å2-0 Å2
3----1.11 Å2
Refinement stepCycle: 1 / Resolution: 1.9→103.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 47 807 5936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.025452
X-RAY DIFFRACTIONr_bond_other_d0.0020.024691
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.97439
X-RAY DIFFRACTIONr_angle_other_deg1.056310941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9415656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67323.977264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76515837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2061521
X-RAY DIFFRACTIONr_chiral_restr0.1180.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216188
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021241
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_it2.1192.2122582
X-RAY DIFFRACTIONr_mcbond_other2.0872.212581
X-RAY DIFFRACTIONr_mcangle_it2.7243.3073252
X-RAY DIFFRACTIONr_mcangle_other2.7263.3083253
X-RAY DIFFRACTIONr_scbond_it2.532.42870
X-RAY DIFFRACTIONr_scbond_other2.5282.42870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.693.5024188
X-RAY DIFFRACTIONr_long_range_B_refined5.3427.0447057
X-RAY DIFFRACTIONr_long_range_B_other5.05526.1726827
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 165 -
Rwork0.264 3588 -
obs--95.57 %

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