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- PDB-3sh5: Calcium-bound Laminin G like domain 3 from human perlecan -

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Basic information

Entry
Database: PDB / ID: 3sh5
TitleCalcium-bound Laminin G like domain 3 from human perlecan
ComponentsLG3 peptide
KeywordsMETAL BINDING PROTEIN / Actin disassambly activity / integrin alpha 2 beta 1
Function / homology
Function and homology information


extracellular matrix structural constituent conferring compression resistance / collagen V binding / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation ...extracellular matrix structural constituent conferring compression resistance / collagen V binding / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / circulatory system development / Laminin interactions / plasma membrane protein complex / negative regulation of cell adhesion / smoothened signaling pathway / low-density lipoprotein particle receptor binding / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / animal organ regeneration / Retinoid metabolism and transport / positive regulation of endothelial cell proliferation / embryo implantation / Degradation of the extracellular matrix / lysosomal lumen / receptor-mediated endocytosis / negative regulation of angiogenesis / brain development / lipid metabolic process / Golgi lumen / amyloid-beta binding / angiogenesis / collagen-containing extracellular matrix / Attachment and Entry / cell differentiation / response to hypoxia / response to xenobiotic stimulus / inflammatory response / Amyloid fiber formation / negative regulation of cell population proliferation / focal adhesion / calcium ion binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain ...Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin G domain / SEA domain profile. / SEA domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / Immunoglobulin domain / LDL receptor-like superfamily / EGF-like domain / Immunoglobulin domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin subtype / Immunoglobulin / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Basement membrane-specific heparan sulfate proteoglycan core protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVan Le, B. / Kim, K.K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of the LG3 Domain of Endorepellin, an Angiogenesis Inhibitor.
Authors: Van Le, B. / Kim, H. / Choi, J. / Kim, J.H. / Hahn, M.J. / Lee, C. / Kim, K.K. / Hwang, H.Y.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LG3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6122
Polymers20,5721
Non-polymers401
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.356, 48.638, 79.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LG3 peptide / Laminin-G like domain 3 / HSPG2


Mass: 20571.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P98160
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.89 Å3/Da / Density % sol: 35.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 8000, 200mM calcium acetate, 100mM MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→29 Å / Num. all: 4115 / Num. obs: 4115 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASESphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.85 / Rfactor Rfree error: 0.021 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.952 / SU ML: 0.313 / Data cutoff high absF: 1065743 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30103 190 4.6 %RANDOM
Rwork0.22144 ---
obs0.22479 3924 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT MODEL
Displacement parametersBiso max: 56.41 Å2 / Biso mean: 22.383 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1-4.71 Å20 Å20 Å2
2---3.26 Å20 Å2
3----1.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.8→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 1 21 1391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211402
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9661906
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3415181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.04123.01663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29615207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4581513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0221106
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7681.5903
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41421442
X-RAY DIFFRACTIONr_scbond_it2.0093499
X-RAY DIFFRACTIONr_scangle_it3.3654.5464
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.803→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 21 -
Rwork0.16 266 -
obs--93.49 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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