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- PDB-1ctn: CRYSTAL STRUCTURE OF A BACTERIAL CHITINASE AT 2.3 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ctn
TitleCRYSTAL STRUCTURE OF A BACTERIAL CHITINASE AT 2.3 ANGSTROMS RESOLUTION
ComponentsCHITINASE A
KeywordsLYASE (OXO-ACID)
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process
Similarity search - Function
Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / 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 ...Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsPerrakis, A. / Tews, I. / Dauter, Z. / Wilson, K.S. / Vorgias, C.E.
Citation
Journal: Structure / Year: 1994
Title: Crystal structure of a bacterial chitinase at 2.3 A resolution.
Authors: Perrakis, A. / Tews, I. / Dauter, Z. / Oppenheim, A.B. / Chet, I. / Wilson, K.S. / Vorgias, C.E.
#1: Journal: CHITIN ENZYMOL. / Year: 1993
Title: Purification and Characterization of the Recombinant Chtin Degrading Enzymes Chitinase a and Chitobiase from Serratia Marcescens
Authors: Vorgias, C.E. / Tews, I. / Perrakis, A. / Oppenheim, A.B. / Wilson, K.S.
#2: Journal: Embo J. / Year: 1986
Title: Isolation and Characterization of Genes Encoding Two Chitinase Enzymes from Serratia Marcescens
Authors: Jones, J.D.G. / Grady, K.L. / Suslow, T.V. / Bedbrook, J.R.
History
DepositionOct 10, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHITINASE A


Theoretical massNumber of molelcules
Total (without water)58,6701
Polymers58,6701
Non-polymers00
Water5,981332
1
A: CHITINASE A

A: CHITINASE A


Theoretical massNumber of molelcules
Total (without water)117,3392
Polymers117,3392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Unit cell
Length a, b, c (Å)203.100, 133.900, 59.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PEPTIDE: GLY 190 - PHE 191 / 2: CIS PEPTIDE: GLU 315 - PHE 316 / 3: CIS PEPTIDE: TRP 539 - GLU 54

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Components

#1: Protein CHITINASE A


Mass: 58669.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: PBR322 DERIVATIVE GENE: / References: UniProt: P07254, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal grow
*PLUS
pH: 7 / Method: microdialysis / Details: Vorgias, C. E., (1992) J. Mol. Bio., 226, 897.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMsodium phosphate11
21 mMEDTA11
3100 mM11NaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 38115 / % possible obs: 97.2 % / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Observed criterion σ(I): 12.5 / Redundancy: 5.2 % / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameClassification
ARP/wARPmodel building
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→10 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.162 -
obs0.162 38115
Displacement parametersBiso mean: 25.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 0 332 4454
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.7793
X-RAY DIFFRACTIONx_mcangle_it3.9615
X-RAY DIFFRACTIONx_scbond_it7.2366
X-RAY DIFFRACTIONx_scangle_it9.6048
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.040.037
X-RAY DIFFRACTIONx_planar_d0.050.045
X-RAY DIFFRACTIONx_plane_restr0.020.014
X-RAY DIFFRACTIONx_chiral_restr0.150.19

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