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- PDB-9fbp: Deletion mutant MmChi60 -

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Basic information

Entry
Database: PDB / ID: 9fbp
TitleDeletion mutant MmChi60
ComponentsChitinase 60
KeywordsHYDROLASE / Chitinase / Deletion mutant / Psychrophilic protein / Protein engineering
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin binding / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / : / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II ...Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / : / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesMoritella marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.844 Å
AuthorsRypniewski, W. / Bejger, M. / Biniek-Antosiak, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2017/27/B/NZ1/02201 Poland
CitationJournal: To Be Published
Title: Probing the structure and thermodynamics of a psychrophilic chitinase
Authors: Bejger, M. / Malecki, P.H. / Biniek-Antosiak, K. / Rypniewski, W.
History
DepositionMay 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase 60
B: Chitinase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2324
Polymers83,1862
Non-polymers462
Water4,017223
1
A: Chitinase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6162
Polymers41,5931
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6162
Polymers41,5931
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.790, 172.829, 47.088
Angle α, β, γ (deg.)90.000, 90.006, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitinase 60


Mass: 41592.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Both Ig-like domains deleted; catalytic domain connected to CBD domain
Source: (gene. exp.) Moritella marina (bacteria) / Strain: MP-1 / Gene: chi60
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B1VBB0, chitinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M sodium malonate, 0.5% Jeffamine ED-2001 and 0.1 M HEPES at pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9171 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2017 / Details: focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9171 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5324
pseudo-merohedral22-h,-k,l20.4676
ReflectionResolution: 1.84→50 Å / Num. obs: 54492 / % possible obs: 88.8 % / Redundancy: 2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.081 / Net I/σ(I): 10.02
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 7740 / CC1/2: 0.691 / Rrim(I) all: 0.577 / % possible all: 78.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.844→47.088 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.927 / SU ML: 0.063 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2192 1007 1.848 %
Rwork0.1545 53484 -
all0.156 --
obs-54491 88.795 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.524 Å2
Baniso -1Baniso -2Baniso -3
1--10.936 Å2-0 Å21.201 Å2
2---2.671 Å20 Å2
3---13.607 Å2
Refinement stepCycle: LAST / Resolution: 1.844→47.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 2 223 6107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0116044
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165406
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6438252
X-RAY DIFFRACTIONr_angle_other_deg0.621.57312426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2425740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.367520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5910914
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.69710314
X-RAY DIFFRACTIONr_chiral_restr0.0920.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021452
X-RAY DIFFRACTIONr_nbd_refined0.2180.21250
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.25208
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22942
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23184
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0510.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1720.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2580.219
X-RAY DIFFRACTIONr_nbd_other0.2280.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.27
X-RAY DIFFRACTIONr_mcbond_it2.7712.5662966
X-RAY DIFFRACTIONr_mcbond_other2.772.5662966
X-RAY DIFFRACTIONr_mcangle_it3.6134.6213704
X-RAY DIFFRACTIONr_mcangle_other3.6134.6223705
X-RAY DIFFRACTIONr_scbond_it2.9982.7623078
X-RAY DIFFRACTIONr_scbond_other2.9972.7633079
X-RAY DIFFRACTIONr_scangle_it4.2094.9984548
X-RAY DIFFRACTIONr_scangle_other4.2094.9984549
X-RAY DIFFRACTIONr_lrange_it5.54527.8756985
X-RAY DIFFRACTIONr_lrange_other5.53727.8916970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.844-1.8920.333490.2283103X-RAY DIFFRACTION69.3815
1.892-1.9440.276530.1973650X-RAY DIFFRACTION83.3633
1.944-20.272810.1843932X-RAY DIFFRACTION94.6462
2-2.0620.288710.1813841X-RAY DIFFRACTION93.6109
2.062-2.1290.193780.1593728X-RAY DIFFRACTION93.4676
2.129-2.2040.216750.153484X-RAY DIFFRACTION92.0352
2.204-2.2870.236660.1443276X-RAY DIFFRACTION89.0725
2.287-2.380.221550.1393385X-RAY DIFFRACTION93.7074
2.38-2.4850.174610.1413213X-RAY DIFFRACTION92.8531
2.485-2.6060.241520.152971X-RAY DIFFRACTION91.5229
2.606-2.7470.211600.1452723X-RAY DIFFRACTION88.6306
2.747-2.9130.187540.1492648X-RAY DIFFRACTION90.7016
2.913-3.1130.177460.1582536X-RAY DIFFRACTION91.1401
3.113-3.3610.227510.1622301X-RAY DIFFRACTION88.9898
3.361-3.680.26410.1642017X-RAY DIFFRACTION86.1088
3.68-4.1110.187390.1421938X-RAY DIFFRACTION89.782
4.111-4.7420.209200.1251684X-RAY DIFFRACTION88.2444
4.742-5.7920.233270.1491365X-RAY DIFFRACTION84.7231
5.792-8.1310.187150.1771107X-RAY DIFFRACTION87.7934
8.131-47.0880.198130.138582X-RAY DIFFRACTION81.1733

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