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- PDB-1ll4: STRUCTURE OF C. IMMITIS CHITINASE 1 COMPLEXED WITH ALLOSAMIDIN -

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Basic information

Entry
Database: PDB / ID: 1ll4
TitleSTRUCTURE OF C. IMMITIS CHITINASE 1 COMPLEXED WITH ALLOSAMIDIN
ComponentsCHITINASE 1
KeywordsHYDROLASE / BETA-ALPHA BARREL / ENZYME-INHIBITOR COMPLEX
Function / homology
Function and homology information


endochitinase activity / chitinase / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
ALLOSAMIZOLINE / : / 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 1.0Sep 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)177,42212
Polymers174,8594
Non-polymers2,5638
Water1,802100
1
A: CHITINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3553
Polymers43,7151
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHITINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3553
Polymers43,7151
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CHITINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3553
Polymers43,7151
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CHITINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3553
Polymers43,7151
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.045, 78.190, 88.457
Angle α, β, γ (deg.)80.61, 82.27, 66.72
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CHITINASE 1


Mass: 43714.812 Da / Num. of mol.: 4 / Fragment: RESIDUES 36-427
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: PIR: JC4565, UniProt: P0CB51*PLUS, chitinase
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DAllpNAcb1-4DAllpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2222h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-AllpNAc]{[(4+1)][b-D-AllpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-AMI / ALLOSAMIZOLINE


Mass: 216.234 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 43.6 %
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
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, sitting drop
Details: Hollis, T., (1998) Acta Crystallogr., Sect.D, 54, 1412.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
24 mg/mlchitinase1drop
30.1 Msodium HEPES1reservoir
430 %PEG40001reservoir
510 %isopropanol1reservoir

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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: Aug 19, 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: 34859 / Num. obs: 34859 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3428 / % possible all: 93.2
Reflection
*PLUS
Rmerge(I) obs: 0.131
Reflection shell
*PLUS
Rmerge(I) obs: 0.369

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1D2K

1d2k


Resolution: 2.8→5 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.258 1188 RANDOM
Rwork0.197 --
all-28561 -
obs-24264 -
Refinement stepCycle: LAST / Resolution: 2.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12332 0 172 100 12604
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg2.996
Refinement
*PLUS
Rfactor Rfree: 0.258 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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