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- PDB-2ox8: Human Scavenger Receptor C-type Lectin carbohydrate-recognition d... -

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Basic information

Entry
Database: PDB / ID: 2ox8
TitleHuman Scavenger Receptor C-type Lectin carbohydrate-recognition domain.
ComponentsScavenger receptor with C-type lectin type I
KeywordsSUGAR BINDING PROTEIN / c-type lectin
Function / homology
Function and homology information


carbohydrate mediated signaling / positive regulation of cell adhesion molecule production / galactose binding / toll-like receptor 3 signaling pathway / low-density lipoprotein particle binding / scavenger receptor activity / phagocytosis, recognition / collagen trimer / Scavenging by Class A Receptors / pattern recognition receptor activity ...carbohydrate mediated signaling / positive regulation of cell adhesion molecule production / galactose binding / toll-like receptor 3 signaling pathway / low-density lipoprotein particle binding / scavenger receptor activity / phagocytosis, recognition / collagen trimer / Scavenging by Class A Receptors / pattern recognition receptor activity / cellular response to exogenous dsRNA / regulation of immune response / receptor-mediated endocytosis / extracellular matrix / defense response / endocytic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / membrane => GO:0016020 / defense response to bacterium / innate immune response / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
CD209-like, C-type lectin-like domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like ...CD209-like, C-type lectin-like domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Collectin-12 / Collectin-12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWeis, W.I. / Feinberg, H. / Drickamer, K. / Taylor, M.E.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Scavenger receptor C-type lectin binds to the leukocyte cell surface glycan Lewis(x) by a novel mechanism.
Authors: Feinberg, H. / Taylor, M.E. / Weis, W.I.
History
DepositionFeb 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Scavenger receptor with C-type lectin type I
B: Scavenger receptor with C-type lectin type I
C: Scavenger receptor with C-type lectin type I
D: Scavenger receptor with C-type lectin type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,56038
Polymers65,8484
Non-polymers1,71234
Water59433
1
A: Scavenger receptor with C-type lectin type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8959
Polymers16,4621
Non-polymers4338
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Scavenger receptor with C-type lectin type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8959
Polymers16,4621
Non-polymers4338
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Scavenger receptor with C-type lectin type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,88510
Polymers16,4621
Non-polymers4239
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Scavenger receptor with C-type lectin type I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,88510
Polymers16,4621
Non-polymers4239
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.422, 80.422, 67.159
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Scavenger receptor with C-type lectin type I


Mass: 16462.012 Da / Num. of mol.: 4 / Fragment: CRD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRCL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BYH7, UniProt: Q5KU26*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.9 Å3/Da / Density % sol: 35.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The protein solution contained 10mg ml-1 protein, 8mM CaCl2 , 8mM Tris pH=7.8, 20mM NaCl and 10mM Lewisx. The reservoir solution contained 8% Peg 8K, 0.2M ZnAc2 and 0.1 M Tris, pH 7.0. , ...Details: The protein solution contained 10mg ml-1 protein, 8mM CaCl2 , 8mM Tris pH=7.8, 20mM NaCl and 10mM Lewisx. The reservoir solution contained 8% Peg 8K, 0.2M ZnAc2 and 0.1 M Tris, pH 7.0. , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30.9 Å / Num. obs: 16533 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 39.9 Å2 / Rsym value: 0.069
Reflection shellResolution: 2.5→2.57 Å / Rsym value: 0.24 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
Blu-Icedata collection
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30.92 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 709657.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.308 840 5.1 %RANDOM
Rwork0.233 ---
obs-16533 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.7607 Å2 / ksol: 0.356584 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å26.01 Å20 Å2
2--2.91 Å20 Å2
3----5.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→30.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4312 0 34 33 4379
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 136 4.9 %
Rwork0.277 2637 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3water_rep.paramion.top

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