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- PDB-7zoi: Carbohydrate binding domain CBM92-A from a multi-catalytic glucan... -

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Basic information

Entry
Database: PDB / ID: 7zoi
TitleCarbohydrate binding domain CBM92-A from a multi-catalytic glucanase-chitinase from Chitinophaga pinensis DSM 2588
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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Glycoside hydrolase superfamily / Mainly Beta
Similarity search - Domain/homology
Glycoside hydrolase family 18
Similarity search - Component
Biological speciesChitinophaga pinensis DSM 2588 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 18


Theoretical massNumber of molelcules
Total (without water)16,2241
Polymers16,2241
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer by size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5770 Å2
Unit cell
Length a, b, c (Å)31.659, 53.712, 56.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 16223.884 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinophaga pinensis DSM 2588 (bacteria)
Gene: Cpin_2580 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A979GQH9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.48 Å3/Da / Density % sol: 17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 5.5 with 10 % w/v PEG 3350, 400 mM NH4SO4, and 10 mM urea

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.991874 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991874 Å / Relative weight: 1
ReflectionResolution: 1.4→38.95 Å / Num. obs: 13501 / % possible obs: 94.2 % / Redundancy: 12.3 % / Biso Wilson estimate: 12.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.3
Reflection shellResolution: 1.4→1.46 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3 / Num. unique obs: 675 / CC1/2: 0.942 / % possible all: 70.1

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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: 1.4→38.95 Å / SU ML: 0.1421 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2476 1348 9.99 %
Rwork0.2051 12142 -
obs0.2093 13490 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.6 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 0 51 990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056970
X-RAY DIFFRACTIONf_angle_d0.87631318
X-RAY DIFFRACTIONf_chiral_restr0.0791135
X-RAY DIFFRACTIONf_plane_restr0.0054175
X-RAY DIFFRACTIONf_dihedral_angle_d20.6981333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.3872540.2335525X-RAY DIFFRACTION29.92
1.45-1.510.237810.2143707X-RAY DIFFRACTION41.06
1.51-1.580.2938960.2312827X-RAY DIFFRACTION47.75
1.58-1.660.2488990.2225897X-RAY DIFFRACTION51.79
1.66-1.760.25341130.21351013X-RAY DIFFRACTION58.16
1.76-1.90.23291280.22471215X-RAY DIFFRACTION69.19
1.9-2.090.24911700.2361523X-RAY DIFFRACTION86.47
2.09-2.40.27551970.22311754X-RAY DIFFRACTION99.69
2.4-3.020.26012030.21411785X-RAY DIFFRACTION99.9
3.02-38.950.22222070.17551896X-RAY DIFFRACTION99.76

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