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- PDB-1cns: CRYSTAL STRUCTURE OF CHITINASE AT 1.91A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1cns
TitleCRYSTAL STRUCTURE OF CHITINASE AT 1.91A RESOLUTION
ComponentsCHITINASE
KeywordsANTIFUNGAL PROTEIN / ALPHA-HELICAL STRUCTURE / ANTI-FUNGAL PROTEIN
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / polysaccharide catabolic process / defense response to fungus / cell wall macromolecule catabolic process
Similarity search - Function
Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily ...Chitinases family 19 signature 1. / Chitinases family 19 signature 2. / Endochitinase; domain 2 / Endochitinase, domain 2 / Glycoside hydrolase, family 19 / Glycoside hydrolase, family 19, catalytic / Chitinase class I / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
26 kDa endochitinase 2
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / Resolution: 1.91 Å
AuthorsSong, H.K. / Suh, S.W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Refined structure of the chitinase from barley seeds at 2.0 a resolution.
Authors: Song, H.K. / Suh, S.W.
#1: Journal: Proteins / Year: 1993
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of Chitinase from Barley Seeds
Authors: Song, H.K. / Hwang, K.Y. / Kim, K.K. / Suh, S.W.
History
DepositionJun 24, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_keywords / 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_keywords.text / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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: CHITINASE
B: CHITINASE


Theoretical massNumber of molelcules
Total (without water)52,1002
Polymers52,1002
Non-polymers00
Water4,071226
1
A: CHITINASE


Theoretical massNumber of molelcules
Total (without water)26,0501
Polymers26,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHITINASE


Theoretical massNumber of molelcules
Total (without water)26,0501
Polymers26,0501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.380, 44.470, 81.490
Angle α, β, γ (deg.)90.00, 111.99, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 164 / 2: CIS PROLINE - PRO B 164
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6431, -0.6782, 0.3556), (-0.6915, 0.315, -0.65), (0.3289, -0.6639, -0.6716)
Vector: -46.323, 51.836, 83.271)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 1 .. B 243 A 1 .. A 243 0.522

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Components

#1: Protein CHITINASE


Mass: 26050.010 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Organ: SEED / Tissue: SEEDS / References: UniProt: P23951, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal
*PLUS
Density % sol: 2.25 %
Crystal grow
*PLUS
pH: 6.23 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %(w/v)PEG30001reservoir
2100 mMsodium citrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: FAST TV-AREA DETECTOR / Detector: AREA DETECTOR / Date: Sep 10, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.91→27.3 Å / Num. obs: 31884 / % possible obs: 86.8 % / Observed criterion σ(I): 0.5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.049
Reflection
*PLUS
Rmerge(I) obs: 0.049

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Processing

Software
NameVersionClassification
MADNESdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.91→8 Å / σ(F): 2
Details: HIS A 121 AND HIS B 121, WHICH ARE WELL DEFINED IN THE ELECTRON DENSITY, ARE IN THE DISALLOWED REGION IN THE RAMACHANDRAN PLOT.
RfactorNum. reflection% reflection
Rfree0.244 -17.7 %
Rwork0.186 --
obs0.186 31038 95.4 %
Displacement parametersBiso mean: 14.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.91→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 0 226 3898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.67
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.67

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