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- PDB-1xku: Crystal structure of the dimeric protein core of decorin, the arc... -

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Basic information

Entry
Database: PDB / ID: 1xku
TitleCrystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan
ComponentsDecorin
KeywordsSTRUCTURAL PROTEIN / Proteoglycan / Leucine-rich repeat
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 / SIRAS / Resolution: 2.15 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 29, 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: Advisory / 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)37,2995
Polymers36,5131
Non-polymers7864
Water2,954164
1
A: Decorin
hetero molecules

A: Decorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,59710
Polymers73,0262
Non-polymers1,5728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)55.780, 124.145, 129.609
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-803-

HOH

DetailsThe second part of the biological assembly is generated by the two-fold axis -x, y, -z+1/2

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Components

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


Mass: 36512.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: DCN / Cell line (production host): HEK 293A / Production host: Homo sapiens (human) / 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.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.31 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: PEG 400, TRIS, OCTYL-BETA-D-GLUCOPYRANOSIDE, SODIUM AZIDE, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 25, 2002
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→33.2 Å / Num. all: 24593 / Num. obs: 24593 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 32.2 Å2 / Rsym value: 0.048 / Net I/σ(I): 8.7
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3266 / Rsym value: 0.367 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.15→33 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.575 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.159 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21747 1253 5.1 %RANDOM
Rwork0.18951 ---
all0.19093 24591 --
obs0.19093 24591 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.491 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2--0.19 Å20 Å2
3----2.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.159 Å0.186 Å
Luzzati d res low-33 Å
Luzzati sigma a-0.102 Å
Refinement stepCycle: LAST / Resolution: 2.15→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 50 164 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222470
X-RAY DIFFRACTIONr_bond_other_d0.0010.021
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.9913352
X-RAY DIFFRACTIONr_angle_other_deg0.53932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.91725.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19915442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.684159
X-RAY DIFFRACTIONr_chiral_restr0.1170.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021797
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021
X-RAY DIFFRACTIONr_nbd_refined0.2140.21016
X-RAY DIFFRACTIONr_nbd_other0.2870.22
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21624
X-RAY DIFFRACTIONr_nbtor_other0.2390.22
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.212
X-RAY DIFFRACTIONr_mcbond_it1.0491.51587
X-RAY DIFFRACTIONr_mcbond_other0.0321.51
X-RAY DIFFRACTIONr_mcangle_it1.63222481
X-RAY DIFFRACTIONr_scbond_it2.9733990
X-RAY DIFFRACTIONr_scangle_it4.7024.5871
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 74 -
Rwork0.244 1545 -
obs-1619 89.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.65190.0091-0.22951.12940.01894.3774-0.06430.05740.01650.022-0.05760.26740.0796-0.74080.1219-0.1527-0.00070.0069-0.0084-0.0448-0.0113-11.953812.133336.2715
21.25810.29580.6583.4785-1.01473.9797-0.0568-0.1930.07460.7388-0.1487-0.2582-0.430.09830.20560.1729-0.0325-0.0327-0.0781-0.0467-0.01742.098116.086968.3309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA22 - 20022 - 200
2X-RAY DIFFRACTION2AA201 - 326201 - 326

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