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

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Basic information

Entry
Database: PDB / ID: 9fbo
TitleDeletion mutant of chitinase MmChi60
Components(Chitinase 60) x 2
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 (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: 2.69 Å
AuthorsMalecki, P.H. / 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: Malecki, P.H. / Bejger, M. / 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)99,6874
Polymers99,4682
Non-polymers2182
Water1448
1
A: Chitinase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9533
Polymers49,7351
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase 60


Theoretical massNumber of molelcules
Total (without water)49,7341
Polymers49,7341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)225.739, 225.739, 65.311
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Chitinase 60


Mass: 49734.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chitinase MmCHi60 with one Ig-like domain missing.,Chitinase MmCHi60 with one Ig-like domain missing.
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: Protein Chitinase 60


Mass: 49733.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Deletion mutant of MmChi60 with one Ig-like domain missing,Deletion mutant of MmChi60 with one Ig-like domain missing
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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% (w/v) PEG 20000, 20% (v/v) PEG MME 550, a mix of monosaccharides: 20 mM of each: D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine and 0.1 M MES/imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 19, 2014 / Details: Focussing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.68→66 Å / Num. obs: 34425 / % possible obs: 98.8 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.099 / Net I/σ(I): 14.1
Reflection shellResolution: 2.68→2.84 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 5271 / CC1/2: 0.929 / Rrim(I) all: 0.926 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→65.165 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 20.036 / SU ML: 0.365 / Cross valid method: FREE R-VALUE / ESU R: 0.624 / ESU R Free: 0.316
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2519 1000 2.92 %
Rwork0.1941 33249 -
all0.196 --
obs-34249 99.333 %
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: 115.581 Å2
Baniso -1Baniso -2Baniso -3
1-2.548 Å21.274 Å2-0 Å2
2--2.548 Å2-0 Å2
3----8.265 Å2
Refinement stepCycle: LAST / Resolution: 2.69→65.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7026 0 13 8 7047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127218
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166473
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.7849862
X-RAY DIFFRACTIONr_angle_other_deg0.5861.75814894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.365890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.337524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.882101098
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.97110366
X-RAY DIFFRACTIONr_chiral_restr0.0770.21070
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021692
X-RAY DIFFRACTIONr_nbd_refined0.2490.21737
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.27045
X-RAY DIFFRACTIONr_nbtor_refined0.1960.23592
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.23863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.26
X-RAY DIFFRACTIONr_metal_ion_refined0.30.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.290.227
X-RAY DIFFRACTIONr_nbd_other0.1940.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.220.22
X-RAY DIFFRACTIONr_mcbond_it10.99611.4423566
X-RAY DIFFRACTIONr_mcbond_other10.9911.4423566
X-RAY DIFFRACTIONr_mcangle_it15.98520.5344454
X-RAY DIFFRACTIONr_mcangle_other15.98920.5334455
X-RAY DIFFRACTIONr_scbond_it10.83911.913652
X-RAY DIFFRACTIONr_scbond_other10.81311.9073650
X-RAY DIFFRACTIONr_scangle_it16.16321.6795408
X-RAY DIFFRACTIONr_scangle_other16.16221.6785409
X-RAY DIFFRACTIONr_lrange_it20.65109.5578354
X-RAY DIFFRACTIONr_lrange_other20.649109.5558355
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
2.69-2.7590.689690.59123070.59425510.8650.87593.13990.61
2.759-2.8350.344720.3824050.37924860.9060.90999.6380.344
2.835-2.9170.352700.3823240.37924010.9270.91499.70850.348
2.917-3.0070.346680.32422740.32523470.9110.92899.7870.271
3.007-3.1050.29670.29522080.29522800.9420.93999.78070.255
3.105-3.2140.37640.28921410.29122090.9140.94499.81890.243
3.214-3.3350.377620.26120430.26421070.8980.94999.90510.221
3.335-3.470.344600.23319890.23620540.9240.96899.75660.208
3.47-3.6240.248570.22619100.22619690.9640.97599.89840.209
3.624-3.8010.261540.19618040.19818590.9620.98199.94620.182
3.801-4.0050.238520.17217270.17417810.9640.98399.88770.162
4.005-4.2470.193490.15716290.15916790.9740.98599.94040.149
4.247-4.5390.224460.14715360.14915840.9680.98699.87370.142
4.539-4.9010.248440.14314420.14614880.9730.98799.86560.144
4.901-5.3660.201390.14613010.14813400.9740.9881000.148
5.366-5.9940.244360.17111890.17312270.9610.98399.8370.174
5.994-6.9110.301310.19410550.19710860.9520.981000.2
6.911-8.4410.285270.1578860.169140.9610.98599.89060.176
8.441-11.8390.15210.1196910.127130.9870.99299.85970.14
11.839-65.1650.129120.1773880.1764030.9930.97599.25560.203

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