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- PDB-9fbs: Deletion mutant of chitinase MmChi60 -

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Basic information

Entry
Database: PDB / ID: 9fbs
TitleDeletion mutant of chitinase MmChi60
ComponentsChitinase 60
KeywordsHYDROLASE / Chitinase / Psychrophilic / Deletion mutant / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / 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: 2.354 Å
AuthorsBejger, M. / Rypniewski, W.
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. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1843
Polymers36,1211
Non-polymers632
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-25 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.764, 74.009, 172.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Chitinase 60


Mass: 36121.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Catalytic domain of chitinase MmChi60 / 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.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) PEG 4000, 0.4 M MgCl2, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 28, 2017 / Details: focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 13787 / % possible obs: 99.3 % / Redundancy: 9.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.152 / Net I/σ(I): 12.7
Reflection shellResolution: 2.35→2.5 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 2113 / CC1/2: 0.762 / Rrim(I) all: 1.015 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.354→43.134 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.794 / SU ML: 0.219 / Cross valid method: FREE R-VALUE / ESU R: 0.465 / ESU R Free: 0.288
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2655 828 6.006 %
Rwork0.1859 12958 -
all0.191 --
obs-13786 99.266 %
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: 42.173 Å2
Baniso -1Baniso -2Baniso -3
1--0.131 Å2-0 Å20 Å2
2---0.018 Å2-0 Å2
3---0.149 Å2
Refinement stepCycle: LAST / Resolution: 2.354→43.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 2 76 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0112617
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162377
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.6573567
X-RAY DIFFRACTIONr_angle_other_deg0.4961.5795460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5965322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.94759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92710402
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.89710136
X-RAY DIFFRACTIONr_chiral_restr0.0680.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023158
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
X-RAY DIFFRACTIONr_nbd_refined0.220.2491
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22135
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21285
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21302
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.261
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.22
X-RAY DIFFRACTIONr_nbd_other0.1470.213
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.22
X-RAY DIFFRACTIONr_mcbond_it3.1484.1741291
X-RAY DIFFRACTIONr_mcbond_other3.1484.1741291
X-RAY DIFFRACTIONr_mcangle_it4.6717.51612
X-RAY DIFFRACTIONr_mcangle_other4.6717.5031613
X-RAY DIFFRACTIONr_scbond_it3.7324.5021326
X-RAY DIFFRACTIONr_scbond_other3.7314.5041327
X-RAY DIFFRACTIONr_scangle_it5.7368.1411955
X-RAY DIFFRACTIONr_scangle_other5.7358.1421956
X-RAY DIFFRACTIONr_lrange_it7.37939.6362870
X-RAY DIFFRACTIONr_lrange_other7.37639.4342867
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.354-2.4150.418550.398500.3929950.9180.91390.95480.392
2.415-2.4810.316580.2829210.2849790.9430.9491000.245
2.481-2.5520.303580.2498970.2539550.9390.9591000.214
2.552-2.6310.355560.2338860.249420.9390.9641000.198
2.631-2.7170.322530.2218230.2288760.9250.9681000.187
2.717-2.8120.38540.1938510.2039060.9280.97599.88960.155
2.812-2.9170.219500.1847750.1868280.9670.97999.63770.151
2.917-3.0360.262480.1867590.198070.9480.9771000.156
3.036-3.170.258480.1857470.1897960.9420.97999.87440.158
3.17-3.3240.255440.1846870.1887320.960.97999.86340.162
3.324-3.5020.225430.1796850.1827280.9730.9821000.158
3.502-3.7130.275420.1736460.1796880.9520.9851000.16
3.713-3.9680.284370.1875850.1936220.9710.9831000.173
3.968-4.2830.232360.165680.1646060.9670.98699.670.152
4.283-4.6870.194340.1285240.1325580.9780.9891000.126
4.687-5.2320.223300.1284770.1335070.9780.991000.125
5.232-6.0270.269270.1634270.1694550.9640.98799.78020.155
6.027-7.3460.256240.183720.1853960.9760.9831000.179
7.346-10.2410.23190.162890.1633080.9750.9871000.169
10.241-43.1340.338120.3561890.3552030.9660.94899.01480.411

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