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- PDB-8ouq: Clr-11 from Rattus norvegicus -

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Basic information

Entry
Database: PDB / ID: 8ouq
TitleClr-11 from Rattus norvegicus
ComponentsC-type lectin domain family 2 member D11
KeywordsIMMUNE SYSTEM / CTLD FOLD / NATURAL KILLER CELL
Function / homology
Function and homology information


natural killer cell lectin-like receptor binding / carbohydrate binding / external side of plasma membrane
Similarity search - Function
: / Natural killer cell receptor-like, C-type lectin-like domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
C-type lectin domain family 2 member D11
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSkalova, T. / Blaha, J. / Kalouskova, B. / Skorepa, O. / Vanek, O. / Dohnalek, J.
Funding support Czech Republic, European Union, 2items
OrganizationGrant numberCountry
Czech Academy of Sciences86652036 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447European Union
CitationJournal: To Be Published
Title: Clr-11 from Rattus norvegicus
Authors: Skalova, T. / Blaha, J. / Kalouskova, B. / Skorepa, O. / Vanek, O. / Dohnalek, J.
History
DepositionApr 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: C-type lectin domain family 2 member D11
BBB: C-type lectin domain family 2 member D11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9014
Polymers31,4582
Non-polymers4422
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint3 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.863, 69.346, 62.473
Angle α, β, γ (deg.)90.000, 96.853, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C-type lectin domain family 2 member D11 / C-type lectin-related protein B / Clr-b / Lectin-like transmembrane protein / Osteoclast inhibitory lectin


Mass: 15729.235 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: STRAIN OF RAT: WAG / Gene: Clec2d11, Clrb, Ocil / Plasmid: PTW5SEC / Cell line (production host): HEK293S GNTI- / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): HUMAN EMBRYONIC KIDNEY / References: UniProt: Q0H8B9
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2 M sodium formate, 0.1 M sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→46.23 Å / Num. obs: 34197 / % possible obs: 99.1 % / Redundancy: 13.8 % / Biso Wilson estimate: 16.1 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.032 / Rrim(I) all: 0.12 / Χ2: 0.98 / Net I/σ(I): 11
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1687 / CC1/2: 0.967 / Rpim(I) all: 0.258 / Rrim(I) all: 0.968 / Χ2: 0.99 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.23 Å / Cor.coef. Fo:Fc: 0.967 / SU B: 1.993 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.096
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 986 3 %random
Rwork0.1903 34084 --
all0.19 ---
obs-34084 98.654 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.127 Å2
Baniso -1Baniso -2Baniso -3
1--1.619 Å20 Å2-0.216 Å2
2--3.067 Å2-0 Å2
3----1.357 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 28 276 2367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132214
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141878
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.663019
X-RAY DIFFRACTIONr_angle_other_deg1.5541.5974321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1015261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.27321.143140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40715336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0271518
X-RAY DIFFRACTIONr_chiral_restr0.1020.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022579
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02621
X-RAY DIFFRACTIONr_nbd_refined0.2160.2414
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21787
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21059
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2991
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2182
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.150.213
X-RAY DIFFRACTIONr_nbd_other0.230.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.230
X-RAY DIFFRACTIONr_mcbond_it2.0621.7591014
X-RAY DIFFRACTIONr_mcbond_other2.0571.7571013
X-RAY DIFFRACTIONr_mcangle_it2.9392.6311273
X-RAY DIFFRACTIONr_mcangle_other2.9392.6331274
X-RAY DIFFRACTIONr_scbond_it3.3652.1881200
X-RAY DIFFRACTIONr_scbond_other3.3642.1881201
X-RAY DIFFRACTIONr_scangle_it5.163.1331742
X-RAY DIFFRACTIONr_scangle_other5.1583.1341743
X-RAY DIFFRACTIONr_lrange_it6.53621.9852676
X-RAY DIFFRACTIONr_lrange_other6.42921.2962615
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.2582488X-RAY DIFFRACTION97.3396
1.642-1.6860.2542449X-RAY DIFFRACTION98.1563
1.686-1.7350.2342357X-RAY DIFFRACTION97.9634
1.735-1.7890.2232306X-RAY DIFFRACTION98.295
1.789-1.8470.2042208X-RAY DIFFRACTION98.4835
1.847-1.9120.2032169X-RAY DIFFRACTION98.5014
1.912-1.9840.2162068X-RAY DIFFRACTION97.7316
1.984-2.0650.1842042X-RAY DIFFRACTION98.7427
2.065-2.1570.171923X-RAY DIFFRACTION99.3798
2.157-2.2620.1831814X-RAY DIFFRACTION97.1612
2.262-2.3840.1691783X-RAY DIFFRACTION98.5083
2.384-2.5290.1781668X-RAY DIFFRACTION99.5227
2.529-2.7030.1781572X-RAY DIFFRACTION99.6829
2.703-2.9190.1831491X-RAY DIFFRACTION99.7992
2.919-3.1970.1911357X-RAY DIFFRACTION99.7794
3.197-3.5730.1681235X-RAY DIFFRACTION99.9191
3.573-4.1230.1621083X-RAY DIFFRACTION99.7238
4.123-5.0450.168949X-RAY DIFFRACTION100
5.045-7.1110.221709X-RAY DIFFRACTION100
7.111-46.230.27413X-RAY DIFFRACTION98.568

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