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- PDB-3bxw: Crystal Structure of Stabilin-1 Interacting Chitinase-Like Protei... -

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Basic information

Entry
Database: PDB / ID: 3bxw
TitleCrystal Structure of Stabilin-1 Interacting Chitinase-Like Protein, SI-CLP
ComponentsChitinase domain-containing protein 1
KeywordsHYDROLASE / TIM barrel / Lysosome / Secreted
Function / homology
Function and homology information


platelet degranulation / oligosaccharide binding / chitin binding / negative regulation of cytokine production involved in inflammatory response / lysosomal lumen / trans-Golgi network / late endosome / Platelet degranulation / carbohydrate metabolic process / lysosome ...platelet degranulation / oligosaccharide binding / chitin binding / negative regulation of cytokine production involved in inflammatory response / lysosomal lumen / trans-Golgi network / late endosome / Platelet degranulation / carbohydrate metabolic process / lysosome / innate immune response / extracellular space / extracellular exosome / extracellular region / membrane / nucleus
Similarity search - Function
3,6-anhydro-alpha-l-galactosidase / Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Helicase, Ruva Protein; domain 3 ...3,6-anhydro-alpha-l-galactosidase / Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Helicase, Ruva Protein; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chitinase domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsMeng, G. / Green, T.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of human stabilin-1 interacting chitinase-like protein (SI-CLP) reveals a saccharide-binding cleft with lower sugar-binding selectivity.
Authors: Meng, G. / Zhao, Y. / Bai, X. / Liu, Y. / Green, T.J. / Luo, M. / Zheng, X.
History
DepositionJan 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Chitinase domain-containing protein 1
A: Chitinase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2034
Polymers90,0112
Non-polymers1922
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-36.9 kcal/mol
Surface area30240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.110, 100.110, 249.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Chitinase domain-containing protein 1 / Stabilin-1-interacting chitinase-like protein / SI-CLP / CHID1


Mass: 45005.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHID1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9BWS9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M(NH4)2SO4, 200mM NaCl, 100mM MgCl2, PH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9745 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 8, 2007
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9745 Å / Relative weight: 1
ReflectionResolution: 2.7→86.711 Å / Num. obs: 40805 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Redundancy: 7.4 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 5.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 2.5 / Num. measured all: 38872 / Num. unique all: 5853 / Rsym value: 0.751 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
CNSrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementResolution: 2.7→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2041 5 %RANDOM
Rwork0.222 ---
all0.243 40805 --
obs0.243 40737 99.9 %-
Solvent computationBsol: 25.68 Å2
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.409 Å20 Å20 Å2
2--9.409 Å20 Å2
3----18.819 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5846 0 10 20 5876
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2951.5
X-RAY DIFFRACTIONc_scbond_it1.8762
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scangle_it2.9792.5
Xplor fileSerial no: 1 / Param file: protein_rep.param

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