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- PDB-1xcd: Dimeric bovine tissue-extracted decorin, crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 1xcd
TitleDimeric bovine tissue-extracted decorin, crystal form 1
ComponentsDecorin
KeywordsSTRUCTURAL PROTEIN / LEUCINE-RICH REPEAT / PROTEOGLYCAN
Function / homology
Function and homology information


A tetrasaccharide linker sequence is required for GAG synthesis / Chondroitin sulfate biosynthesis / Dermatan sulfate biosynthesis / CS/DS degradation / ECM proteoglycans / negative regulation of collagen fibril organization / collagen fibril binding / Degradation of the extracellular matrix / negative regulation of vascular endothelial growth factor signaling pathway / glycosaminoglycan binding ...A tetrasaccharide linker sequence is required for GAG synthesis / Chondroitin sulfate biosynthesis / Dermatan sulfate biosynthesis / CS/DS degradation / ECM proteoglycans / negative regulation of collagen fibril organization / collagen fibril binding / Degradation of the extracellular matrix / negative regulation of vascular endothelial growth factor signaling pathway / glycosaminoglycan binding / negative regulation of endothelial cell migration / extracellular matrix binding / positive regulation of mitochondrial fission / positive regulation of mitochondrial depolarization / positive regulation of macroautophagy / negative regulation of angiogenesis / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Small leucine-rich proteoglycan, class I, decorin/asporin/byglycan / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeats, bacterial type / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype ...Small leucine-rich proteoglycan, class I, decorin/asporin/byglycan / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeats, bacterial type / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.31 Å
AuthorsScott, P.G. / McEwan, P.A. / Dodd, C.M. / Bergmann, E.M. / Bishop, P.N. / Bella, J.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Crystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan
Authors: Scott, P.G. / McEwan, P.A. / Dodd, C.M. / Bergmann, E.M. / Bishop, P.N. / Bella, J.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Light and X-ray scattering show decorin to be a dimer in solution
Authors: Scott, P.G. / Grossmann, J.G. / Dodd, C.M. / Sheehan, J.K. / Bishop, P.N.
History
DepositionSep 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Decorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2926
Polymers36,3841
Non-polymers9085
Water2,324129
1
A: Decorin
hetero molecules

A: Decorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,58312
Polymers72,7682
Non-polymers1,81610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)55.380, 124.110, 129.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-500-

HOH

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Components

#1: Protein Decorin / / Bone proteoglycan II / PG-S2


Mass: 36383.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Extracted from calf skin under denaturing conditions and refolded
Source: (natural) Bos taurus (cattle) / References: UniProt: P21793
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.1 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: PEG 400, Tris, beta-octyl-D-glucoside, sodium azide, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2001
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→55.9 Å / Num. obs: 20012 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 35.6 Å2 / Rsym value: 0.044 / Net I/σ(I): 11.6
Reflection shellResolution: 2.31→2.43 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2875 / Rsym value: 0.212 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.31→33.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1988687.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1897 5 %RANDOM
Rwork0.222 ---
all0.251 20040 --
obs0.222 19940 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.7186 Å2 / ksol: 0.305406 e/Å3
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1-13.95 Å20 Å20 Å2
2---3.97 Å20 Å2
3----9.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.31→33.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 58 129 2558
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 2.31→2.45 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 319 5.1 %
Rwork0.282 5898 -
obs-5898 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TMN.PARAMTMN.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP

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