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

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Basic information

Entry
Database: PDB / ID: 9fbq
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 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MALONATE ION / chitinase
Similarity search - Component
Biological speciesMoritella marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2694
Polymers36,1211
Non-polymers1483
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-19 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.114, 72.590, 174.883
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-798-

HOH

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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 MmChi60, a chitiniase from Moritella marina
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: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 45% (v/v) MPD, 0.2 M ammonium acetate, 0.1 M Bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 19, 2014 / Details: focusing mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 54649 / % possible obs: 99.6 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.086 / Net I/σ(I): 14.17
Reflection shellResolution: 1.48→1.57 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 8529 / CC1/2: 0.635 / Rrim(I) all: 0.877 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→19.671 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.743 / SU ML: 0.063 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2065 1039 1.901 %
Rwork0.1764 53610 -
all0.177 --
obs-54649 99.624 %
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: 17.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.499 Å2-0 Å20 Å2
2--0.189 Å2-0 Å2
3---0.309 Å2
Refinement stepCycle: LAST / Resolution: 1.48→19.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 9 354 2914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122662
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162413
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.6583635
X-RAY DIFFRACTIONr_angle_other_deg0.6061.5795554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.57959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47510413
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.77110139
X-RAY DIFFRACTIONr_chiral_restr0.0870.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02636
X-RAY DIFFRACTIONr_nbd_refined0.2420.2558
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.22274
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21330
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2258
X-RAY DIFFRACTIONr_metal_ion_refined0.1370.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.217
X-RAY DIFFRACTIONr_nbd_other0.1330.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.237
X-RAY DIFFRACTIONr_mcbond_it1.6791.7591303
X-RAY DIFFRACTIONr_mcbond_other1.6751.761303
X-RAY DIFFRACTIONr_mcangle_it2.413.1621630
X-RAY DIFFRACTIONr_mcangle_other2.4153.1651631
X-RAY DIFFRACTIONr_scbond_it2.4771.9761359
X-RAY DIFFRACTIONr_scbond_other2.4661.9721356
X-RAY DIFFRACTIONr_scangle_it3.7573.5291999
X-RAY DIFFRACTIONr_scangle_other3.7563.532000
X-RAY DIFFRACTIONr_lrange_it5.46221.4123231
X-RAY DIFFRACTIONr_lrange_other5.41420.7543210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.5160.311730.3013753X-RAY DIFFRACTION95.6979
1.516-1.5580.343730.2773780X-RAY DIFFRACTION100
1.558-1.6020.323720.263732X-RAY DIFFRACTION100
1.602-1.6510.285710.2443629X-RAY DIFFRACTION100
1.651-1.7050.234680.2323514X-RAY DIFFRACTION100
1.705-1.7650.245650.2233365X-RAY DIFFRACTION100
1.765-1.8310.245630.223267X-RAY DIFFRACTION100
1.831-1.9050.277610.2063156X-RAY DIFFRACTION100
1.905-1.9890.228590.23019X-RAY DIFFRACTION99.9675
1.989-2.0850.232560.1952901X-RAY DIFFRACTION100
2.085-2.1960.194540.1792791X-RAY DIFFRACTION100
2.196-2.3270.223510.1722648X-RAY DIFFRACTION100
2.327-2.4860.193480.1622454X-RAY DIFFRACTION100
2.486-2.6810.228450.1612309X-RAY DIFFRACTION100
2.681-2.9320.171410.1682155X-RAY DIFFRACTION100
2.932-3.2690.189380.1561941X-RAY DIFFRACTION100
3.269-3.7570.202340.1441745X-RAY DIFFRACTION100
3.757-4.560.117290.1151499X-RAY DIFFRACTION100
4.56-6.2820.147230.1271199X-RAY DIFFRACTION100
6.282-19.6710.124150.16752X-RAY DIFFRACTION100

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