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- PDB-1ll6: STRUCTURE OF THE D169N MUTANT OF C. IMMITIS CHITINASE 1 -

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Basic information

Entry
Database: PDB / ID: 1ll6
TitleSTRUCTURE OF THE D169N MUTANT OF C. IMMITIS CHITINASE 1
ComponentsCHITINASE 1
KeywordsHYDROLASE / BETA-ALPHA BARREL
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region
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
Endochitinase 1 / Endochitinase 1
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBortone, K. / Monzingo, A.F. / Ernst, S. / Robertus, J.D.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: THE STRUCTURE OF AN ALLOSAMIDIN COMPLEX WITH THE COCCIDIOIDES IMMITIS CHITINASE DEFINES A ROLE FOR A SECOND ACID RESIDUE IN SUBSTRATE-ASSISTED MECHANISM
Authors: BORTONE, K. / MONZINGO, A.F. / ERNST, S. / ROBERTUS, J.D.
History
DepositionApr 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHITINASE 1
B: CHITINASE 1
C: CHITINASE 1
D: CHITINASE 1


Theoretical massNumber of molelcules
Total (without water)174,8554
Polymers174,8554
Non-polymers00
Water77543
1
A: CHITINASE 1


Theoretical massNumber of molelcules
Total (without water)43,7141
Polymers43,7141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHITINASE 1


Theoretical massNumber of molelcules
Total (without water)43,7141
Polymers43,7141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CHITINASE 1


Theoretical massNumber of molelcules
Total (without water)43,7141
Polymers43,7141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CHITINASE 1


Theoretical massNumber of molelcules
Total (without water)43,7141
Polymers43,7141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.890, 78.180, 88.430
Angle α, β, γ (deg.)80.51, 82.13, 66.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CHITINASE 1


Mass: 43713.824 Da / Num. of mol.: 4 / Fragment: RESIDUES 36-427 / Mutation: D169N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (fungus) / Gene: CTS1 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli)
References: UniProt: P54196, UniProt: P0CB51*PLUS, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, ISOPROPANOL, SODIUM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 3, 2000
RadiationMonochromator: DOUBLE FOCUSSING MIRRORS (NI & PT) + NI FILTER
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 34083 / Num. obs: 34083 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 6.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3261 / % possible all: 89.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1LL4

1ll4


Resolution: 2.8→5 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.256 826 RANDOM
Rwork0.182 --
all-26551 -
obs-16310 -
Refinement stepCycle: LAST / Resolution: 2.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12332 0 0 43 12375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg2.978

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