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- PDB-6f8n: Key residues affecting transglycosylation activity in family 18 c... -

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Basic information

Entry
Database: PDB / ID: 6f8n
TitleKey residues affecting transglycosylation activity in family 18 chitinases - Insights into donor and acceptor subsites
ComponentsGlycoside hydrolase family 18
KeywordsHYDROLASE / Chitooligosaccharides / Degree of polymerization / Hydrolysis / Transglycosylation / Chitinase / CARBOHYDRATE
Function / homology
Function and homology information


chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
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 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 ...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 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glycoside hydrolase family 18
Similarity search - Component
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMadhuprakash, J. / Dalhus, B. / Swaroopa Rani, T. / Podile, A.R. / Eijsink, V.G.H. / Sorlie, M.
Funding support Norway, India, 3items
OrganizationGrant numberCountry
Research Council of Norway221576, 247001 and 247730 Norway
South-Eastern Norway Regional Health Authority2015095 Norway
DST-INSPIRE-Faculty awardIFA16-LSPA 40 India
CitationJournal: Biochemistry / Year: 2018
Title: Key Residues Affecting Transglycosylation Activity in Family 18 Chitinases: Insights into Donor and Acceptor Subsites.
Authors: Madhuprakash, J. / Dalhus, B. / Rani, T.S. / Podile, A.R. / Eijsink, V.G.H. / Sorlie, M.
History
DepositionDec 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_struct_special_symmetry / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 18
B: Glycoside hydrolase family 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,68310
Polymers91,5152
Non-polymers1,1688
Water17,925995
1
A: Glycoside hydrolase family 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3415
Polymers45,7581
Non-polymers5844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3415
Polymers45,7581
Non-polymers5844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.840, 87.570, 75.390
Angle α, β, γ (deg.)90.00, 115.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-752-

HOH

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Components

#1: Protein Glycoside hydrolase family 18 /


Mass: 45757.508 Da / Num. of mol.: 2 / Mutation: E153Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (strain 568) (bacteria)
Strain: 568 / Gene: Spro_2725 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8GFD6
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 995 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl pH 7.0 and 10% (w/v) PEG 8000 in mixtures containing (GlcNAc)6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.45→69.96 Å / Num. obs: 126010 / % possible obs: 93.9 % / Redundancy: 2.8 % / Rrim(I) all: 0.078 / Net I/σ(I): 9.9
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4074 / Rrim(I) all: 0.436 / % possible all: 60.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NZC

4nzc


Resolution: 1.45→69.96 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.01
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 6194 4.92 %Random
Rwork0.1749 ---
obs0.1766 126003 93.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→69.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6228 0 76 995 7299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066498
X-RAY DIFFRACTIONf_angle_d0.8468837
X-RAY DIFFRACTIONf_dihedral_angle_d17.5262335
X-RAY DIFFRACTIONf_chiral_restr0.08959
X-RAY DIFFRACTIONf_plane_restr0.0061143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4476-1.46410.35831350.32692476X-RAY DIFFRACTION59
1.4641-1.48130.34441200.31862801X-RAY DIFFRACTION66
1.4813-1.49940.36031660.29663065X-RAY DIFFRACTION72
1.4994-1.51830.30011780.29033226X-RAY DIFFRACTION78
1.5183-1.53830.30221920.2833594X-RAY DIFFRACTION84
1.5383-1.55940.28941790.2743850X-RAY DIFFRACTION91
1.5594-1.58170.33612190.2594144X-RAY DIFFRACTION98
1.5817-1.60530.26352060.24214201X-RAY DIFFRACTION99
1.6053-1.63040.2691760.23294269X-RAY DIFFRACTION100
1.6304-1.65710.24552030.23014263X-RAY DIFFRACTION100
1.6571-1.68570.24212070.2174247X-RAY DIFFRACTION100
1.6857-1.71630.25452120.21134207X-RAY DIFFRACTION100
1.7163-1.74940.24332250.19764234X-RAY DIFFRACTION100
1.7494-1.78510.22412020.19294231X-RAY DIFFRACTION100
1.7851-1.82390.23572270.18764202X-RAY DIFFRACTION99
1.8239-1.86630.21522270.17874210X-RAY DIFFRACTION99
1.8663-1.9130.20552350.1734196X-RAY DIFFRACTION99
1.913-1.96470.18772140.17454211X-RAY DIFFRACTION99
1.9647-2.02250.20462050.17174252X-RAY DIFFRACTION99
2.0225-2.08780.22462370.16524197X-RAY DIFFRACTION99
2.0878-2.16240.18852140.1594225X-RAY DIFFRACTION99
2.1624-2.2490.20772130.15444173X-RAY DIFFRACTION98
2.249-2.35140.18062220.15794202X-RAY DIFFRACTION99
2.3514-2.47540.19882150.16234147X-RAY DIFFRACTION98
2.4754-2.63050.22022490.17384124X-RAY DIFFRACTION97
2.6305-2.83360.20332080.17054102X-RAY DIFFRACTION96
2.8336-3.11870.19792210.16124198X-RAY DIFFRACTION98
3.1187-3.570.19312310.14854149X-RAY DIFFRACTION98
3.57-4.49770.15772220.13374180X-RAY DIFFRACTION97
4.4977-70.03760.18492340.15394233X-RAY DIFFRACTION97

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