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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
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: 2.69 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
Revision 2.0Oct 22, 2025Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _cell.Z_PDB / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _pdbx_entity_nonpoly.entity_id / _pdbx_entry_details.has_ligand_of_interest / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _refine.B_iso_mean / _refine.aniso_B[1][3] / _refine.aniso_B[2][3] / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.solvent_model_details / _refine_hist.d_res_low / _struct_asym.entity_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_label_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Description: Sequence discrepancy
Details: The present structure is a deletion mutant with 82 residues missing. An offset of 82 was added to residues 423-468, chains A and B, for consistency with the native structure of this protein. ...Details: The present structure is a deletion mutant with 82 residues missing. An offset of 82 was added to residues 423-468, chains A and B, for consistency with the native structure of this protein. In addition, an error in sequence was corrected: residue 153, chain B, now is Glu, not Gln.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,6884
Polymers99,4692
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)49,7351
Polymers49,7351
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, 90, 120
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Chitinase 60


Mass: 49734.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Source: (gene. exp.) Moritella marina (bacteria) / Strain: MP-1 / Gene: chi60
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: chitinase
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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→65.17 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.252 1000 -
Rwork0.194 --
obs-34249 99.3 %
Displacement parametersBiso mean: 115.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.548 Å21.274 Å20 Å2
2--2.548 Å20 Å2
3----8.265 Å2
Refinement stepCycle: LAST / Resolution: 2.69→65.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7026 0 13 8 7047
LS refinement shellResolution: 2.69→2.76 Å /
Rfactor% reflection
Rfree0.689 -
Rwork0.591 -
obs-93.14 %

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