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

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Basic information

Entry
Database: PDB / ID: 7zoh
TitleCarbohydrate binding domain CBM92-B 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


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Actin-crosslinking / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glycoside hydrolase family 18
Similarity search - Component
Biological speciesChitinophaga pinensis DSM 2588 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / 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 / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_database_related / struct / struct_conf / 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.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 18
B: Glycoside hydrolase family 18
C: Glycoside hydrolase family 18
D: Glycoside hydrolase family 18


Theoretical massNumber of molelcules
Total (without water)64,7074
Polymers64,7074
Non-polymers00
Water5,639313
1
A: Glycoside hydrolase family 18


Theoretical massNumber of molelcules
Total (without water)16,1771
Polymers16,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 18


Theoretical massNumber of molelcules
Total (without water)16,1771
Polymers16,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside hydrolase family 18


Theoretical massNumber of molelcules
Total (without water)16,1771
Polymers16,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside hydrolase family 18


Theoretical massNumber of molelcules
Total (without water)16,1771
Polymers16,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.041, 59.064, 68.032
Angle α, β, γ (deg.)90.978, 92.548, 105.635
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 16176.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: succinimide observed substituted at Asp
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.: 313 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citrate buffer pH 5.5 with 15 % 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: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.56→33.97 Å / Num. obs: 69506 / % possible obs: 95.35 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.42 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.74
Reflection shellResolution: 1.56→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 6543 / CC1/2: 0.415 / % possible all: 88.81

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
BALBESphasing
ARP/wARPmodel building
PHENIX1.15.2_3472refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LLP

3llp


Resolution: 1.56→33.97 Å / SU ML: 0.1833 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.826
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2062 4974 7.16 %
Rwork0.1752 64479 -
obs0.1774 69453 95.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.11 Å2
Refinement stepCycle: LAST / Resolution: 1.56→33.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 0 313 4237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00594080
X-RAY DIFFRACTIONf_angle_d0.9215543
X-RAY DIFFRACTIONf_chiral_restr0.0571556
X-RAY DIFFRACTIONf_plane_restr0.0055742
X-RAY DIFFRACTIONf_dihedral_angle_d21.65131423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.34561250.32171709X-RAY DIFFRACTION75.91
1.58-1.590.31951750.30222109X-RAY DIFFRACTION94.65
1.59-1.610.30021660.2742164X-RAY DIFFRACTION93.69
1.61-1.630.32481430.26672125X-RAY DIFFRACTION95.53
1.63-1.660.29211700.24912133X-RAY DIFFRACTION94.58
1.66-1.680.24541730.2262154X-RAY DIFFRACTION95.33
1.68-1.70.26511720.21252163X-RAY DIFFRACTION94.69
1.7-1.730.23541630.20292104X-RAY DIFFRACTION95.33
1.73-1.750.25441760.19822160X-RAY DIFFRACTION94.96
1.75-1.780.25441620.20522179X-RAY DIFFRACTION95.82
1.78-1.810.22881630.19982123X-RAY DIFFRACTION95.25
1.81-1.850.21811800.18892180X-RAY DIFFRACTION96.05
1.85-1.880.21351540.1812169X-RAY DIFFRACTION95.83
1.88-1.920.2231730.18642133X-RAY DIFFRACTION95.72
1.92-1.960.21771700.19262173X-RAY DIFFRACTION96.34
1.96-2.010.24571770.18252188X-RAY DIFFRACTION96.37
2.01-2.060.2021700.17552145X-RAY DIFFRACTION96.34
2.06-2.110.19361800.17572201X-RAY DIFFRACTION96.71
2.11-2.180.20471580.17752134X-RAY DIFFRACTION96.79
2.18-2.250.20551740.17522201X-RAY DIFFRACTION96.54
2.25-2.330.19671560.17822174X-RAY DIFFRACTION96.64
2.33-2.420.21891670.17812208X-RAY DIFFRACTION96.35
2.42-2.530.2211660.18322149X-RAY DIFFRACTION96.54
2.53-2.660.22251720.19252199X-RAY DIFFRACTION96.74
2.66-2.830.22921470.19652199X-RAY DIFFRACTION96.11
2.83-3.050.21691670.18762173X-RAY DIFFRACTION97.06
3.05-3.350.18611640.16162188X-RAY DIFFRACTION96.83
3.35-3.840.19011810.14972163X-RAY DIFFRACTION96.66
3.84-4.840.16141590.13352216X-RAY DIFFRACTION97.14
4.84-33.970.1971710.17522163X-RAY DIFFRACTION96.49

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