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

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Basic information

Entry
Database: PDB / ID: 9fbr
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: 1.743 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)36,6615
Polymers36,1211
Non-polymers5404
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-17 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.499, 74.086, 175.569
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-765-

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.: 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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% (w/v) Poly(acrylic acid sodium salt) average Mw ~5100 Da, 0.02 M MgCl2, 0.1 M HEPES pH 7.5, with N,N',N'', N'''-tetraacetylchitotetraose (NAG4 )

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9168 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2019 / Details: focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9168 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 33204 / % possible obs: 97.4 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.099 / Net I/σ(I): 9.97
Reflection shellResolution: 1.74→1.85 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.854 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 5274 / CC1/2: 0.603 / Rrim(I) all: 0.99 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.743→43.892 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.498 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2223 1030 3.102 %
Rwork0.1764 32174 -
all0.178 --
obs-33204 97.364 %
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: 24.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.521 Å2-0 Å2-0 Å2
2--0.871 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.743→43.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 32 288 2871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122669
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162424
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.6623643
X-RAY DIFFRACTIONr_angle_other_deg0.5251.5785579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.39659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4210405
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.65810138
X-RAY DIFFRACTIONr_chiral_restr0.0780.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined0.2340.2550
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22257
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21334
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21413
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2210
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.29
X-RAY DIFFRACTIONr_nbd_other0.1970.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.214
X-RAY DIFFRACTIONr_mcbond_it2.0652.4641297
X-RAY DIFFRACTIONr_mcbond_other2.0542.4651297
X-RAY DIFFRACTIONr_mcangle_it3.0184.4181621
X-RAY DIFFRACTIONr_mcangle_other3.0174.4221622
X-RAY DIFFRACTIONr_scbond_it3.0282.7541372
X-RAY DIFFRACTIONr_scbond_other2.9642.7471370
X-RAY DIFFRACTIONr_scangle_it4.534.9382019
X-RAY DIFFRACTIONr_scangle_other4.5294.9412020
X-RAY DIFFRACTIONr_lrange_it6.58426.3093159
X-RAY DIFFRACTIONr_lrange_other6.47324.9473088
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
1.743-1.7890.445750.41723390.41825040.8980.91396.40580.413
1.789-1.8370.339730.36622710.36523920.9460.9397.99330.352
1.837-1.8910.322720.29922510.29923700.9270.94898.01690.281
1.891-1.9490.293700.27521920.27523180.9470.95297.58410.247
1.949-2.0120.266640.2420110.24122060.9510.96394.06160.208
2.012-2.0830.273650.2220190.22121260.9550.96898.02450.19
2.083-2.1610.278640.220000.20320900.9480.97498.7560.174
2.161-2.2490.241610.17819020.1820120.9620.9897.56460.155
2.249-2.3490.204590.17418460.17519380.970.98198.29720.152
2.349-2.4630.23550.16917460.1718300.9680.98198.41530.147
2.463-2.5960.254520.16216010.16517490.9580.98394.51120.142
2.596-2.7530.205510.15815900.1616690.9740.98498.32230.14
2.753-2.9420.207480.1515150.15215750.970.98799.23810.138
2.942-3.1770.169460.16214220.16314880.9840.98698.65590.153
3.177-3.4780.169400.16212790.16313490.9860.98797.77610.157
3.478-3.8860.203360.14211250.14412340.9840.98994.08430.143
3.886-4.4810.191340.12410560.12511050.9840.99198.64250.132
4.481-5.4740.207290.1298930.1319420.9890.99297.87690.139
5.474-7.6820.213220.176790.1727470.9840.9993.8420.183
7.682-43.8920.186140.1674370.1684580.9830.98598.47160.189

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