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- PDB-5bzj: Crystal structure of the murine cd44 hyaluronan binding domain co... -

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Basic information

Entry
Database: PDB / ID: 5bzj
TitleCrystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule
ComponentsCD44 antigen
KeywordsPROTEIN BINDING / Link module
Function / homology
Function and homology information


Hyaluronan uptake and degradation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / branching involved in prostate gland morphogenesis / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall ...Hyaluronan uptake and degradation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / branching involved in prostate gland morphogenesis / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process / wound healing involved in inflammatory response / positive regulation of adaptive immune response / positive regulation of neutrophil apoptotic process / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / negative regulation of CD4-positive, alpha-beta T cell proliferation / cargo receptor activity / wound healing, spreading of cells / epidermal growth factor receptor binding / branching involved in ureteric bud morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / channel regulator activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / regulation of cell growth / phosphoprotein binding / cytokine-mediated signaling pathway / Wnt signaling pathway / negative regulation of inflammatory response / positive regulation of peptidyl-tyrosine phosphorylation / neuron projection development / transmembrane signaling receptor activity / cell migration / positive regulation of peptidyl-serine phosphorylation / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / membrane raft / apical plasma membrane / external side of plasma membrane / positive regulation of gene expression / protein kinase binding / cell surface / protein-containing complex / extracellular region / plasma membrane
Similarity search - Function
CD44 antigen / CD44 antigen-like / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Chem-4WN / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsLiu, L.K. / Finzel, B.C.
CitationJournal: To Be Published
Title: Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule
Authors: Liu, L.K. / Finzel, B.C.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD44 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3825
Polymers16,8561
Non-polymers5274
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.871, 81.503, 32.181
Angle α, β, γ (deg.)90.000, 118.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CD44 antigen / Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / ...Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / Hermes antigen / Hyaluronate receptor / Lymphocyte antigen 24 / Ly-24 / Phagocytic glycoprotein 1 / PGP-1 / Phagocytic glycoprotein I / PGP-I


Mass: 16855.803 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, unp residues 21-171 / Mutation: H23M; Q24N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd44, Ly-24 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15379
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-4WN / 2-[2-(1-methyl-1H-imidazol-2-yl)ethyl]-1,2,3,4-tetrahydroisoquinolin-8-amine


Mass: 256.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG MME 5000, MES, (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
311
ReflectionResolution: 1.4→81.503 Å / Num. obs: 26735 / % possible obs: 97 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 12 / Num. measured all: 89871
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique all% possible all
1.4-1.4053.50.14989525895.9
6.497-81.5033.30.07788926994.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→40.87 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.2005 / FOM work R set: 0.8897 / SU B: 1.014 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0693 / SU Rfree: 0.0698 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 1308 4.9 %RANDOM
Rwork0.1836 ---
obs0.1848 25307 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.02 Å2 / Biso mean: 11.436 Å2 / Biso min: 3.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0.5 Å2
2--0.72 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 1.4→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 33 83 1287
Biso mean--23.64 17.36 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211317
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9661812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2995169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16824.44463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7715202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.872158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211044
X-RAY DIFFRACTIONr_mcbond_it0.8731.5808
X-RAY DIFFRACTIONr_mcangle_it1.50321331
X-RAY DIFFRACTIONr_scbond_it2.3093509
X-RAY DIFFRACTIONr_scangle_it3.6084.5481
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 90 -
Rwork0.245 1811 -
all-1901 -
obs--95.72 %

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