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- PDB-7zop: Carbohydrate binding domain CBM92-B from a multi-catalytic glucan... -

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Basic information

Entry
Database: PDB / ID: 7zop
TitleCarbohydrate binding domain CBM92-B from a multi-catalytic glucanase-chitinase from Chitinophaga pinensis DSM 2588 in complex with sophorose.
ComponentsGlycoside hydrolase family 18
KeywordsCARBOHYDRATE / beta-trefoil / carbohydrate binding domain / beta-glycan
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase activity / chitin binding / cell surface / extracellular region
Similarity search - Function
Secretion system C-terminal sorting domain / Actin-crosslinking / Secretion system C-terminal sorting domain / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. ...Secretion system C-terminal sorting domain / Actin-crosslinking / Secretion system C-terminal sorting domain / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / Glycoside hydrolase family 18
Similarity search - Component
Biological speciesChitinophaga pinensis DSM 2588 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsMazurkewich, S. / McKee, L.S. / Lu, Z. / Branden, G. / Larsbrink, J.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2017-04906 Sweden
Knut and Alice Wallenberg FoundationWWSC Sweden
CitationJournal: Nat Commun / Year: 2024
Title: Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to beta-glucans.
Authors: Hao, M.S. / Mazurkewich, S. / Li, H. / Kvammen, A. / Saha, S. / Koskela, S. / Inman, A.R. / Nakajima, M. / Tanaka, N. / Nakai, H. / Branden, G. / Bulone, V. / Larsbrink, J. / McKee, L.S.
History
DepositionApr 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2May 8, 2024Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_database_related / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct.title / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 18
B: Glycoside hydrolase family 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5343
Polymers32,3532
Non-polymers1801
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.389, 113.049, 70.902
Angle α, β, γ (deg.)90.000, 98.949, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1252-

HOH

21A-1263-

HOH

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Components

#1: Protein Glycoside hydrolase family 18 / CBM92-B


Mass: 16176.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Succinimide substitution observed at Asp
Source: (gene. exp.) Chitinophaga pinensis DSM 2588 (bacteria)
Gene: Cpin_2580 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A979GQH9
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 with 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976259 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976259 Å / Relative weight: 1
ReflectionResolution: 1.68→43.99 Å / Num. obs: 18228 / % possible obs: 87.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.76 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6
Reflection shellResolution: 1.68→1.86 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 911 / CC1/2: 0.473 / % possible all: 47.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZOH

7zoh


Resolution: 1.68→43.99 Å / SU ML: 0.2509 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.3902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 1821 10 %
Rwork0.2134 16394 -
obs0.2185 18215 54.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.71 Å2
Refinement stepCycle: LAST / Resolution: 1.68→43.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 12 102 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752049
X-RAY DIFFRACTIONf_angle_d1.00922783
X-RAY DIFFRACTIONf_chiral_restr0.0585284
X-RAY DIFFRACTIONf_plane_restr0.0042369
X-RAY DIFFRACTIONf_dihedral_angle_d22.0624715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.730.378920.352721X-RAY DIFFRACTION0.91
1.73-1.780.4277160.3407135X-RAY DIFFRACTION6.11
1.78-1.840.384400.3229363X-RAY DIFFRACTION15.65
1.84-1.90.338730.279656X-RAY DIFFRACTION28.29
1.9-1.980.34941030.2775926X-RAY DIFFRACTION39.91
1.98-2.070.30621220.25321114X-RAY DIFFRACTION47.81
2.07-2.180.32921410.26431263X-RAY DIFFRACTION54.36
2.18-2.320.29831620.26661455X-RAY DIFFRACTION62.29
2.32-2.490.30291790.27211607X-RAY DIFFRACTION69.25
2.49-2.750.29032110.25951899X-RAY DIFFRACTION80.78
2.75-3.140.29032480.24022243X-RAY DIFFRACTION95.99
3.14-3.960.23652610.18922343X-RAY DIFFRACTION99.96
3.96-43.990.2252630.16612369X-RAY DIFFRACTION99.92

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