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- PDB-1dv8: CRYSTAL STRUCTURE OF THE CARBOHYDRATE RECOGNITION DOMAIN OF THE H... -

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Basic information

Entry
Database: PDB / ID: 1dv8
TitleCRYSTAL STRUCTURE OF THE CARBOHYDRATE RECOGNITION DOMAIN OF THE H1 SUBUNIT OF THE ASIALOGLYCOPROTEIN RECEPTOR
ComponentsASIALOGLYCOPROTEIN RECEPTOR 1
KeywordsSIGNALING PROTEIN / C-type lectin CRD
Function / homology
Function and homology information


asialoglycoprotein receptor activity / Asparagine N-linked glycosylation / fucose binding / : / D-mannose binding / receptor-mediated endocytosis / signaling receptor activity / external side of plasma membrane / extracellular region / identical protein binding ...asialoglycoprotein receptor activity / Asparagine N-linked glycosylation / fucose binding / : / D-mannose binding / receptor-mediated endocytosis / signaling receptor activity / external side of plasma membrane / extracellular region / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Hepatic lectin, N-terminal domain / CD209-like, C-type lectin-like domain / 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) ...Hepatic lectin, N-terminal domain / CD209-like, C-type lectin-like domain / 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
Asialoglycoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMeier, M. / Bider, M.D. / Malashkevich, V.N. / Spiess, M. / Burkhard, P.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of the carbohydrate recognition domain of the H1 subunit of the asialoglycoprotein receptor.
Authors: Meier, M. / Bider, M.D. / Malashkevich, V.N. / Spiess, M. / Burkhard, P.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Mechanism of N-Acetylgalactosamine Binding to a C-type Animal Lectin Carbohydrate-recognition Domain
Authors: Kolatkar, A.R. / Leung, A.K. / Isecke, R. / Brossmer, R. / Drickamer, K. / Weis, W.I.
History
DepositionJan 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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: ASIALOGLYCOPROTEIN RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3215
Polymers15,1651
Non-polymers1564
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.720, 32.460, 40.820
Angle α, β, γ (deg.)90.00, 91.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1004-

CL

21A-7-

HOH

31A-29-

HOH

41A-66-

HOH

51A-81-

HOH

61A-92-

HOH

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Components

#1: Protein ASIALOGLYCOPROTEIN RECEPTOR 1 / HEPATIC LECTIN H1


Mass: 15165.472 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN - H1 SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: PARENCHYM / Cell: HEPATOCYTE / Organ: LIVER / Plasmid: PET3B (NOVAGEN) / Production host: Escherichia coli (E. coli) / References: UniProt: P07306
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, ammonium sulfate, cacodylate, Tris-HCl, sodium chloride, calcium chloride, lactose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.8
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.8 mg/mlprotein1drop
220 mMTris-HCl1drop
3120 mM1dropNaCl
42 mM1dropCaCl2
520 mMlactose1drop
625 %PEG80001reservoir
780 mMammonium sulfate1reservoir
8100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 25, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 7412 / Num. obs: 7342 / % possible obs: 95.9 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.317 / Num. unique all: 2132 / % possible all: 95.9
Reflection shell
*PLUS
% possible obs: 95.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS0.5refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.3→19.35 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 959133.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 551 8.6 %RANDOM
Rwork0.195 ---
all-6425 --
obs-6425 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.01 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å2-7.25 Å2
2--4.2 Å20 Å2
3----2.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 4 104 1180
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 102 9.5 %
Rwork0.227 971 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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