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- PDB-5bzh: Crystal structure of the murine CD44 hyaluronan binding domain co... -

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Basic information

Entry
Database: PDB / ID: 5bzh
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 degradation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / wound healing involved in inflammatory response / hyaluronan catabolic process ...Hyaluronan degradation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / wound healing involved in inflammatory response / hyaluronan catabolic process / positive regulation of adaptive immune response / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / channel regulator activity / negative regulation of CD4-positive, alpha-beta T cell proliferation / wound healing, spreading of cells / cargo receptor activity / branching involved in ureteric bud morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / microvillus / negative regulation of DNA damage response, signal transduction by p53 class mediator / lamellipodium membrane / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / negative regulation of inflammatory response / Wnt signaling pathway / cytokine-mediated signaling pathway / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / membrane raft / external side of plasma membrane / positive regulation of gene expression / cell surface / 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
3-(3,4-dihydroisoquinolin-2(1H)-yl)propan-1-amine / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD44 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1243
Polymers16,8561
Non-polymers2682
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.850, 81.720, 32.120
Angle α, β, γ (deg.)90.000, 117.970, 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 / 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-4X1 / 3-(3,4-dihydroisoquinolin-2(1H)-yl)propan-1-amine


Mass: 190.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 42.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG MME 5000, 100 mM MES, 200 mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→8.72 Å / Num. obs: 9978 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.753 % / Biso Wilson estimate: 15.378 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.017 / Rrim(I) all: 0.02 / Χ2: 0.99 / Net I/σ(I): 56.83 / Num. measured all: 37452
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-20.9990.03333.9625187727220.0493.5
2-2.050.9990.03137.1826477437050.03694.9
2.05-2.110.9990.02642.8825467016730.03196
2.11-2.180.9990.02743.4325677196790.03294.4
2.18-2.250.9990.02348.924466676460.02796.9
2.25-2.330.9990.02250.3124346726450.02696
2.33-2.420.9990.02152.2222666235970.02595.8
2.42-2.520.9990.02152.3922696125960.02497.4
2.52-2.630.9990.0254.8621115815550.02495.5
2.63-2.760.9990.0254.1620925605510.02398.4
2.76-2.910.9990.01860.4820065495280.02196.2
2.91-3.0810.01565.3218755034920.01897.8
3.08-3.2910.01570.4117584734610.01797.5
3.29-3.5610.01374.2416794544430.01597.6
3.56-3.910.01380.0214964033980.01598.8
3.9-4.3610.01386.6913603733630.01597.3
4.36-5.0310.01389.4611933213170.01598.8
5.03-6.1610.01481.1110582962870.01697
6.16-8.7210.01581.157442102060.01898.1
8.7210.01389.383871251140.01691.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→8.72 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.2181 / WRfactor Rwork: 0.167 / FOM work R set: 0.8629 / SU B: 3.338 / SU ML: 0.099 / SU R Cruickshank DPI: 0.183 / SU Rfree: 0.1666 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 524 5.3 %RANDOM
Rwork0.1702 ---
obs0.1732 9425 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.44 Å2 / Biso mean: 9.05 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.16 Å2
2---0.12 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.95→8.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 18 53 1242
Biso mean--20.22 11.15 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221236
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.951683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94623.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85815192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.942159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021957
X-RAY DIFFRACTIONr_mcbond_it0.7071.5760
X-RAY DIFFRACTIONr_mcangle_it1.2821240
X-RAY DIFFRACTIONr_scbond_it2.1733476
X-RAY DIFFRACTIONr_scangle_it3.5424.5443
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 32 -
Rwork0.163 685 -
all-717 -
obs--94.97 %

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