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- PDB-4ptm: Crystal Structure of Chitinase D from Serratia proteamaculans in ... -

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Basic information

Entry
Database: PDB / ID: 4ptm
TitleCrystal Structure of Chitinase D from Serratia proteamaculans in complex with N-acetyl glucosamine, a hydrolyzed product of hexasaccharide at 1.7 Angstrom resolution
ComponentsGlycoside hydrolase family 18
KeywordsHYDROLASE / Chitinase D / Chitinase / Glycoside hydrolase / Chtin / N-acetyl glucosamine
Function / homology
Function and homology information


chitinase / chitin catabolic process / 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. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain ...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. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / chitinase
Similarity search - Component
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKushwaha, G.S. / Madhuprakash, J. / Singh, A. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Podile, A.R. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of Chitinase D from Serratia proteamaculans in complex with N-acetyl glucosamine, a hydrolyzed product of hexasaccharide at 1.7 Angstrom resolution
Authors: Kushwaha, G.S. / Madhuprakash, J. / Singh, A. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Podile, A.R. / Singh, T.P.
History
DepositionMar 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Data collection / Derived calculations / Category: reflns / reflns_shell / struct_conn
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9785
Polymers44,5141
Non-polymers4644
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.418, 74.064, 88.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Glycoside hydrolase family 18


Mass: 44514.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (bacteria) / Strain: 568 / Gene: Spro_2725 / Production host: Escherichia coli (E. coli) / References: UniProt: A8GFD6, chitinase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M SODIUM FORMATE, 0.1M SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2013 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→59.42 Å / Num. all: 43061 / Num. obs: 43061 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.034 / Net I/σ(I): 5.5
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.89 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LGX

4lgx


Resolution: 1.7→59.42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.295 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 2174 5 %RANDOM
Rwork0.16713 ---
obs0.16841 41221 99.04 %-
all-43061 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.977 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å2-0 Å20 Å2
2---0.64 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→59.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 0 31 336 3479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193229
X-RAY DIFFRACTIONr_bond_other_d0.0060.023030
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9654393
X-RAY DIFFRACTIONr_angle_other_deg0.95436964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1735401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49124.595148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15615507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2491514
X-RAY DIFFRACTIONr_chiral_restr0.1170.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02750
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7691.6171596
X-RAY DIFFRACTIONr_mcbond_other1.7531.6151594
X-RAY DIFFRACTIONr_mcangle_it2.6722.4141993
X-RAY DIFFRACTIONr_mcangle_other2.5712.3871983
X-RAY DIFFRACTIONr_scbond_it2.9151.941633
X-RAY DIFFRACTIONr_scbond_other2.9261.9231624
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5092.7522384
X-RAY DIFFRACTIONr_long_range_B_refined6.16414.3153925
X-RAY DIFFRACTIONr_long_range_B_other6.16414.3183926
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 141 -
Rwork0.261 2751 -
obs--90.83 %

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