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- PDB-1e6n: Chitinase B from Serratia marcescens inactive mutant E144Q in com... -

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Basic information

Entry
Database: PDB / ID: 1e6n
TitleChitinase B from Serratia marcescens inactive mutant E144Q in complex with N-acetylglucosamine-pentamer
ComponentsCHITINASE B
KeywordsHYDROLASE / CHITIN DEGRADATION / GLYCOSIDASE
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region
Similarity search - Function
Carbohydrate-binding module superfamily 5/12 / Seminal Fluid Protein PDC-109 (Domain B) / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily ...Carbohydrate-binding module superfamily 5/12 / Seminal Fluid Protein PDC-109 (Domain B) / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Ribbon / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chitinase B / chitinase
Similarity search - Component
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKomander, D. / Synstad, B. / Eijsink, V.G.H. / Van Aalten, D.M.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structural Insights Into the Catalytic Mechanism of a Family 18 Exo-Chitinase
Authors: Van Aalten, D.M.F. / Komander, D. / Synstad, B. / Gseidnes, S. / Peter, M.G. / Eijsink, V.G.H.
History
DepositionAug 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2001Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHITINASE B
B: CHITINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,34717
Polymers111,0342
Non-polymers3,31315
Water7,945441
1
A: CHITINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,32010
Polymers55,5171
Non-polymers1,8029
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHITINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0277
Polymers55,5171
Non-polymers1,5106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.732, 104.476, 186.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein CHITINASE B


Mass: 55517.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q54276, UniProt: P11797*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1033.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSOME RESIDUES MISSING TO ACCOUNT FOR MISSING DENSITY

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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: 2.5 Å3/Da / Density % sol: 50.6 %
Crystal growpH: 7 / Details: 2.0M AMMONIUM SULFATE, 20% GLYCEROL, HEPES PH 7.0
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Details: Van Aalten, D.M.F., (2000) Proc. Natl. Acad. Sci. U.S.A., 97, 5842.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMcitrate1reservoir
30.5 M1reservoirLi2SO4
40.25 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 27, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. obs: 47907 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 1 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 4.7 / % possible all: 63.1
Reflection
*PLUS
Num. measured all: 123855
Reflection shell
*PLUS
% possible obs: 63.1 % / Redundancy: 2 % / Num. unique obs: 3349 / Num. measured obs: 6725

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E15

1e15


Resolution: 2.25→38.58 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2614827.16 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 985 2.1 %RANDOM
Rwork0.189 ---
obs0.189 47782 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.532 Å2 / ksol: 0.358937 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å20 Å20 Å2
2--6.76 Å20 Å2
3----10.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.25→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7784 0 208 441 8433
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 129 2 %
Rwork0.245 6441 -
obs--76.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMGOL.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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