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

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Basic information

Entry
Database: PDB / ID: 5bzc
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
4,4-dimethyl-1,2,3,4-tetrahydroisoquinoline / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 13, 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 / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _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)17,0793
Polymers16,8401
Non-polymers2392
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.970, 81.940, 32.060
Angle α, β, γ (deg.)90.000, 117.910, 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: 16839.693 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, unp RESIDUES 21-171
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-4WT / 4,4-dimethyl-1,2,3,4-tetrahydroisoquinoline


Mass: 161.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
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: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→40.97 Å / Num. obs: 10233 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.864 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.114 / Χ2: 0.948 / Net I/σ(I): 14.37 / Num. measured all: 39128
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
1.94-1.990.8780.3823.4323187636730.44888.2
1.99-2.050.9050.3514.3628697677430.40796.9
2.05-2.10.9340.2915.1727127227020.33897.2
2.1-2.170.950.2336.3227407337080.2796.6
2.17-2.240.9620.2147.0325476756540.24896.9
2.24-2.320.9680.1848.2625896806690.21498.4
2.32-2.410.9740.178.8824116396200.19897
2.41-2.50.9780.1689.123706316140.19597.3
2.5-2.620.9810.13310.9722585945810.15597.8
2.62-2.740.9850.12611.7421985755690.14799
2.74-2.890.9920.09714.4320675455330.11297.8
2.89-3.070.9960.06918.3319095024950.0898.6
3.07-3.280.9960.05822.2318594974850.06797.6
3.28-3.540.9970.04626.6217584634560.05498.5
3.54-3.880.9980.03931.0815484154050.04597.6
3.88-4.340.9990.03335.5214163733720.03999.7
4.34-5.010.9990.03137.2812233293230.03698.2
5.01-6.140.9980.03632.1410972942910.04199
6.14-8.680.9990.03432.468092212180.0498.6
8.680.9990.02441.974301271220.02996.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.8 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.66 Å
Translation2.5 Å19.66 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
XSCALEdata scaling
PHASER2.1.4phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→40.97 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.2021 / WRfactor Rwork: 0.1641 / FOM work R set: 0.8629 / SU B: 3.613 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1881 / SU Rfree: 0.1665 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / 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
Rfree0.2317 530 5.2 %RANDOM
Rwork0.1816 ---
obs0.1841 9618 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.19 Å2 / Biso mean: 11.037 Å2 / Biso min: 2.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.33 Å2
2--0.57 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.95→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 16 54 1241
Biso mean--12.23 13.18 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221222
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.951666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14424.06859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77915189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.027158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021944
X-RAY DIFFRACTIONr_mcbond_it0.721.5754
X-RAY DIFFRACTIONr_mcangle_it1.25921229
X-RAY DIFFRACTIONr_scbond_it2.1853468
X-RAY DIFFRACTIONr_scangle_it3.5284.5437
LS refinement shellResolution: 1.946→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 35 -
Rwork0.206 658 -
all-693 -
obs--92.52 %

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