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- PDB-4nzc: Crystal structure of Chitinase D from Serratia proteamaculans at ... -

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Basic information

Entry
Database: PDB / ID: 4nzc
TitleCrystal structure of Chitinase D from Serratia proteamaculans at 1.45 Angstrom resolution
ComponentsGlycoside hydrolase family 18
KeywordsHYDROLASE / Chitinase D / TIM barrel / Transglycosylation
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. / 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 / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Glycoside hydrolase family 18
Similarity search - Component
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMadhuprakash, J. / Singh, A. / Kumar, S. / Sinha, M. / Kaur, P. / Sharma, S. / Podile, A.R. / Singh, T.P.
CitationJournal: Int J Biochem Mol Biol / Year: 2013
Title: Structure of chitinase D from Serratia proteamaculans reveals the structural basis of its dual action of hydrolysis and transglycosylation
Authors: Madhuprakash, J. / Singh, A. / Kumar, S. / Sinha, M. / Kaur, P. / Sharma, S. / Podile, A.R. / Singh, T.P.
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3645
Polymers44,0291
Non-polymers3354
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.334, 75.276, 86.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-901-

HOH

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Components

#1: Protein Glycoside hydrolase family 18


Mass: 44028.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (bacteria) / Strain: 568 / Gene: Spro_2725 / Plasmid: pET-22b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
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: MARRESEARCH / Detector: CCD / Date: Jun 21, 2013 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→59.4 Å / Num. all: 69368 / Num. obs: 69368 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.099 / Net I/σ(I): 9.8
Reflection shellResolution: 1.45→1.5 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.316 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LGX

4lgx


Resolution: 1.45→59.4 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.152 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21299 3503 5 %RANDOM
Rwork0.19935 ---
obs0.20006 65876 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.495 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0 Å2
2---0.14 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.45→59.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 0 22 587 3721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193226
X-RAY DIFFRACTIONr_bond_other_d0.0010.023029
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9614388
X-RAY DIFFRACTIONr_angle_other_deg0.77236967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0795403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47924.595148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50115508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7641514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213709
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02751
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_it0.7761.0491601
X-RAY DIFFRACTIONr_mcbond_other0.7711.0481599
X-RAY DIFFRACTIONr_mcangle_it1.3251.5712000
X-RAY DIFFRACTIONr_mcangle_other1.3261.5722001
X-RAY DIFFRACTIONr_scbond_it1.0691.1761625
X-RAY DIFFRACTIONr_scbond_other1.0681.1761625
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7211.712386
X-RAY DIFFRACTIONr_long_range_B_refined5.48310.8344395
X-RAY DIFFRACTIONr_long_range_B_other5.48210.8384396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 229 -
Rwork0.242 4835 -
obs--99.98 %

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