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- PDB-4zy9: X-ray crystal structure of selenomethionine-labelled V110M mutant... -

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Basic information

Entry
Database: PDB / ID: 4zy9
TitleX-ray crystal structure of selenomethionine-labelled V110M mutant 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. / NedA-like, galactose-binding domain / 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 ...Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / NedA-like, galactose-binding domain / 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 III domain / 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 / SAD / Resolution: 1.2 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 21, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucanase/chitosanase
B: Glucanase/chitosanase


Theoretical massNumber of molelcules
Total (without water)30,3582
Polymers30,3582
Non-polymers00
Water10,160564
1
A: Glucanase/chitosanase


Theoretical massNumber of molelcules
Total (without water)15,1791
Polymers15,1791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucanase/chitosanase


Theoretical massNumber of molelcules
Total (without water)15,1791
Polymers15,1791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.233, 65.329, 69.887
Angle α, β, γ (deg.)90.00, 97.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucanase/chitosanase


Mass: 15179.149 Da / Num. of mol.: 2 / Fragment: UNP residues 530-659 / Mutation: V110M
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium fluoride, PEG 3350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97865 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97865 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 78378 / % possible obs: 99.8 % / Redundancy: 6.1 % / Net I/σ(I): 28.4
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 4.5 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.2→47.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 0.846 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24921 1994 2.6 %RANDOM
Rwork0.2083 ---
obs0.20934 75932 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.041 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å2-0.33 Å2
2---0.1 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.2→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 564 2620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.022260
X-RAY DIFFRACTIONr_bond_other_d0.0020.021989
X-RAY DIFFRACTIONr_angle_refined_deg2.4661.8983121
X-RAY DIFFRACTIONr_angle_other_deg1.02934580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6395305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70323.704108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33815321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.161513
X-RAY DIFFRACTIONr_chiral_restr0.1550.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022697
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02584
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_it1.2720.9011125
X-RAY DIFFRACTIONr_mcbond_other1.270.91122
X-RAY DIFFRACTIONr_mcangle_it1.7621.3551414
X-RAY DIFFRACTIONr_mcangle_other1.7621.3551415
X-RAY DIFFRACTIONr_scbond_it1.670.9961135
X-RAY DIFFRACTIONr_scbond_other1.6690.9961136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3881.4521689
X-RAY DIFFRACTIONr_long_range_B_refined5.46510.0563241
X-RAY DIFFRACTIONr_long_range_B_other4.8528.3752818
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 134 -
Rwork0.258 5374 -
obs--94.2 %

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