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- PDB-1chk: STREPTOMYCES N174 CHITOSANASE PH5.5 298K -

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Basic information

Entry
Database: PDB / ID: 1chk
TitleSTREPTOMYCES N174 CHITOSANASE PH5.5 298K
ComponentsCHITOSANASE
KeywordsHYDROLASE (O-GLYCOSYL) / ANTI-FUNGAL PROTEIN / HYDROLASE / O-GLYCOSYL
Function / homology
Function and homology information


chitosanase / chitosanase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitosanase; Chain A, domain 2 / Chitosanase, subunit A, domain 2 / Chitosanases families 46 and 80 active sites signature. / Chitosanase, subunit A; domain 1 / Chitosanase, subunit A, domain 1 / Glycoside hydrolase, family 46, N-terminal / Glycosyl hydrolase family 46 / Glycoside hydrolase, family 46 / Lysozyme-like domain superfamily / Up-down Bundle ...Chitosanase; Chain A, domain 2 / Chitosanase, subunit A, domain 2 / Chitosanases families 46 and 80 active sites signature. / Chitosanase, subunit A; domain 1 / Chitosanase, subunit A, domain 1 / Glycoside hydrolase, family 46, N-terminal / Glycosyl hydrolase family 46 / Glycoside hydrolase, family 46 / Lysozyme-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsMarcotte, E.M. / Robertus, J.D.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: X-ray structure of an anti-fungal chitosanase from streptomyces N174.
Authors: Marcotte, E.M. / Monzingo, A.F. / Ernst, S.R. / Brzezinski, R. / Robertus, J.D.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of a Chitosanase from Streptomyces N174
Authors: Marcotte, E. / Hart, P.J. / Boucher, I. / Brzezinski, R. / Robertus, J.D.
History
DepositionJun 12, 1995Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHITOSANASE
B: CHITOSANASE


Theoretical massNumber of molelcules
Total (without water)51,6982
Polymers51,6982
Non-polymers00
Water91951
1
A: CHITOSANASE


Theoretical massNumber of molelcules
Total (without water)25,8491
Polymers25,8491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHITOSANASE


Theoretical massNumber of molelcules
Total (without water)25,8491
Polymers25,8491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.300, 59.300, 85.400
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.593133, -0.777506, -0.208994), (-0.776563, 0.483989, 0.403367), (-0.212469, 0.401547, -0.890852)
Vector: 58.7539, 21.9874, 36.3579)

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Components

#1: Protein CHITOSANASE / ENDOCHITOSANASE


Mass: 25848.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: N174 / Description: SECRETED (MATURE PEPTIDE) / Gene: CSN / Plasmid: PRL270 / Gene (production host): CSN / Production host: Streptomyces lividans (bacteria) / References: UniProt: P33665
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Marcotte, E., (1993) J.Mol.Biol., 232, 995.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
220 mMsodium acetate1drop
30.5 Mpotassium phosphate1drop
420 %(w/v)PEG80001drop
50.5 Mpotassium phosphate1reservoir
620 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 29, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 21903 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.0885
Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 98.7 % / Num. measured all: 121478

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.4→5 Å / σ(F): 4
RfactorNum. reflection% reflection
Rfree0.175 -0.236 %
Rwork0.181 --
obs0.181 19182 98.7 %
Refinement stepCycle: LAST / Resolution: 2.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 0 51 3691
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.12
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 0.236 % / Rfactor obs: 0.1809 / Rfactor Rfree: 0.1748 / Rfactor Rwork: 0.1809
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg3.118
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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