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- PDB-1xec: Dimeric bovine tissue-extracted decorin, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 1xec
TitleDimeric bovine tissue-extracted decorin, crystal form 2
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 depolarization / positive regulation of mitochondrial fission / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 9, 2004Deposition site: RCSB / Processing site: RCSB
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 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 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
Remark 290 CRYSTALLOGRAPHIC SYMMETRY SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 SYMOP SYMMETRY NNNMMM ... CRYSTALLOGRAPHIC SYMMETRY SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 SYMOP SYMMETRY NNNMMM OPERATOR 1555 X,Y,Z 2555 1/2-X,-Y,1/2+Z 3555 -X,1/2+Y,1/2-Z 4555 1/2+X,1/2-Y,-Z WHERE NNN -> OPERATOR NUMBER MMM -> TRANSLATION VECTOR CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY RELATED MOLECULES. SMTRY1 1 1.000000 0.000000 0.000000 0.00000 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 SMTRY1 2 -1.000000 0.000000 0.000000 26.35050 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 SMTRY3 2 0.000000 0.000000 1.000000 64.85600 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 SMTRY2 3 0.000000 1.000000 0.000000 60.47600 SMTRY3 3 0.000000 0.000000 -1.000000 64.85600 SMTRY1 4 1.000000 0.000000 0.000000 26.35050 SMTRY2 4 0.000000 -1.000000 0.000000 60.47600 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK: NULL

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decorin
B: Decorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2807
Polymers72,7682
Non-polymers1,5125
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.701, 120.952, 129.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 36383.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: PROTEIN WAS EXTRACTED FROM CALF SKIN UNDER DENATURING CONDITIONS AND REFOLDED
Source: (natural) Bos taurus (cattle) / Organ: skin / References: UniProt: P21793
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.97 Å3/Da / Density % sol: 58.2 %
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: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2001 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→19.73 Å / Num. all: 37599 / Num. obs: 37599 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 31.6 Å2 / Rsym value: 0.09 / Net I/σ(I): 6.3
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 3024 / Rsym value: 0.199 / % possible all: 83.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
CNS1.1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XKU

1xku


Resolution: 2.3→19.73 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1680211.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3659 10.1 %RANDOM
Rwork0.214 ---
all0.262 37599 --
obs0.234 36358 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.5121 Å2 / ksol: 0.2985 e/Å3
Displacement parametersBiso mean: 48.4 Å2
Baniso -1Baniso -2Baniso -3
1-19.19 Å20 Å20 Å2
2---1.21 Å20 Å2
3----17.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4742 0 98 298 5138
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_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it2.592
X-RAY DIFFRACTIONc_scangle_it3.972.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 538 10.1 %
Rwork0.303 4782 -
obs-5330 86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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