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- PDB-4zxe: X-ray crystal structure of chitosan-binding module 1 derived from... -

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Basic information

Entry
Database: PDB / ID: 4zxe
TitleX-ray crystal structure of chitosan-binding module 1 derived from chitosanase/glucanase from Paenibacillus sp. IK-5.
ComponentsGlucanase/Chitosanase
KeywordsHYDROLASE / chitosan / CBM32 / chitosanase/glucanase / b-sandwich
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily ...Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose-binding domain-like / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPaenibacillus fukuinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsShinya, S. / Oi, H. / Kitaoku, Y. / Ohnuma, T. / Numata, T. / Fukamizo, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science, and TechnologyS1101035 Japan
CitationJournal: Biochem.J. / Year: 2016
Title: Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase
Authors: Shinya, S. / Nishimura, S. / Kitaoku, Y. / Numata, T. / Kimoto, H. / Kusaoke, H. / Ohnuma, T. / Fukamizo, T.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Glucanase/Chitosanase
B: Glucanase/Chitosanase
C: Glucanase/Chitosanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,66125
Polymers45,1603
Non-polymers1,50122
Water11,259625
1
A: Glucanase/Chitosanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3365
Polymers15,0531
Non-polymers2824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area6010 Å2
MethodPISA
2
B: Glucanase/Chitosanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5228
Polymers15,0531
Non-polymers4687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area6070 Å2
MethodPISA
3
C: Glucanase/Chitosanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,80412
Polymers15,0531
Non-polymers75111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.054, 45.591, 57.581
Angle α, β, γ (deg.)111.69, 105.36, 97.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glucanase/Chitosanase


Mass: 15053.294 Da / Num. of mol.: 3 / Fragment: UNP residues 530-659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus fukuinensis (bacteria)
Description: Paenibacillus fukuinensis has been renamed to Paenibacillus sp. IK-5.
Production host: Escherichia coli (E. coli) / References: UniProt: Q93IE7, cellulase, chitosanase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, Magnesium chloride, MES, PEG8000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50.26 Å / Num. obs: 69228 / % possible obs: 95.1 % / Redundancy: 7.9 % / Net I/σ(I): 1.8
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 8 % / Rmerge(I) obs: 0.069 / Mean I/σ(I) obs: 34.2 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→50.26 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.8 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17179 3478 5 %RANDOM
Rwork0.1432 ---
obs0.14464 65749 95.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.514 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0.18 Å2-0.05 Å2
2--0.13 Å20.02 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 92 625 3798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.023446
X-RAY DIFFRACTIONr_bond_other_d0.0040.023059
X-RAY DIFFRACTIONr_angle_refined_deg2.4141.9124728
X-RAY DIFFRACTIONr_angle_other_deg1.03437037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3525463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.54623.62163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34715485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4991521
X-RAY DIFFRACTIONr_chiral_restr0.150.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02867
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_it0.9930.6461673
X-RAY DIFFRACTIONr_mcbond_other0.9930.6451670
X-RAY DIFFRACTIONr_mcangle_it1.4550.9682102
X-RAY DIFFRACTIONr_mcangle_other1.4550.9682103
X-RAY DIFFRACTIONr_scbond_it1.8650.8371773
X-RAY DIFFRACTIONr_scbond_other1.8320.821758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5281.1522571
X-RAY DIFFRACTIONr_long_range_B_refined5.5887.5884568
X-RAY DIFFRACTIONr_long_range_B_other5.5887.5894569
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 263 -
Rwork0.164 4587 -
obs--91.06 %

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