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- PDB-3sh4: Laminin G like domain 3 from human perlecan -

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Basic information

Entry
Database: PDB / ID: 3sh4
TitleLaminin G like domain 3 from human perlecan
ComponentsLG3 peptide
KeywordsMETAL BINDING PROTEIN / Actin disassambly / integrin alpha12 beta1
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 / Laminin interactions / circulatory system development / plasma membrane protein complex / negative regulation of cell adhesion / low-density lipoprotein particle receptor binding / smoothened signaling pathway / RSV-host interactions / Respiratory syncytial virus (RSV) attachment and entry / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / animal organ regeneration / Integrin cell surface interactions / Retinoid metabolism and transport / positive regulation of endothelial cell proliferation / embryo implantation / Degradation of the extracellular matrix / lysosomal lumen / negative regulation of angiogenesis / receptor-mediated endocytosis / brain development / lipid metabolic process / Golgi lumen / amyloid-beta binding / angiogenesis / collagen-containing extracellular matrix / Attachment and Entry / cell differentiation / response to hypoxia / inflammatory response / response to xenobiotic stimulus / 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 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. / Immunoglobulin domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / 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 / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / 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 / MAD / Resolution: 1.5 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 15, 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


Theoretical massNumber of molelcules
Total (without water)20,5721
Polymers20,5721
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.950, 54.655, 64.353
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.71 Å3/Da / Density % sol: 27.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3.5M sodium formate, 0.1 sodium acetate pH4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→41.67 Å / Num. all: 23231 / Num. obs: 22563 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.5→33.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.485 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 1155 5.1 %RANDOM
Rwork0.1768 ---
obs0.1787 22563 97.12 %-
all-23231 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.58 Å2 / Biso mean: 16.5469 Å2 / Biso min: 5.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 0 202 1653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211487
X-RAY DIFFRACTIONr_angle_refined_deg2.2341.9632023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4015194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39723.38268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71415216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4821513
X-RAY DIFFRACTIONr_chiral_restr0.1580.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0221182
X-RAY DIFFRACTIONr_mcbond_it1.4481.5961
X-RAY DIFFRACTIONr_mcangle_it2.42221532
X-RAY DIFFRACTIONr_scbond_it3.6953526
X-RAY DIFFRACTIONr_scangle_it5.7114.5491
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 70 -
Rwork0.231 1520 -
all-1590 -
obs--93.58 %

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