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- PDB-7ytq: Human langerin carbohydrate recognition domain in complex with an... -

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Basic information

Entry
Database: PDB / ID: 7ytq
TitleHuman langerin carbohydrate recognition domain in complex with an alpha-mannoside ligand
Components
  • CD207 molecule
  • SER-TRP
KeywordsSUGAR BINDING PROTEIN / Langerin / lectin / innate immunity / C-type
Function / homology
Function and homology information


carbohydrate binding / defense response to virus / external side of plasma membrane
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / 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
Chem-JMI / TRYPTOPHAN / CD207 molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWangkanont, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Chulalongkorn University Thailand
CitationJournal: To Be Published
Title: Human langerin carbohydrate recognition domain in complex with an alpha-mannoside ligand
Authors: Wangkanont, K.
History
DepositionAug 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 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
A: CD207 molecule
B: CD207 molecule
C: CD207 molecule
D: CD207 molecule
E: SER-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,16319
Polymers72,0875
Non-polymers2,07614
Water11,890660
1
A: CD207 molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3664
Polymers17,9491
Non-polymers4173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7430 Å2
MethodPISA
2
B: CD207 molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3664
Polymers17,9491
Non-polymers4173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7510 Å2
MethodPISA
3
C: CD207 molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5705
Polymers17,9491
Non-polymers6214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7060 Å2
MethodPISA
4
D: CD207 molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5705
Polymers17,9491
Non-polymers6214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7290 Å2
MethodPISA
5
E: SER-TRP


  • defined by author&software
  • 291 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2911
Polymers2911
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.030, 80.030, 90.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

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Components

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Protein / Protein/peptide , 2 types, 5 molecules ABCDE

#1: Protein
CD207 molecule


Mass: 17949.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD207 / Production host: Escherichia coli (E. coli) / References: UniProt: G3QPX8
#2: Protein/peptide SER-TRP


Mass: 291.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 674 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-JMI / ~{N}-[2-[4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethyl]ethanamide


Mass: 341.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H23NO7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES, 200 mM MgCl2, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→19.94 Å / Num. obs: 74724 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.033 / Rrim(I) all: 0.092 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
8.76-19.946.80.054274390.9970.0230.05991.9
1.6-1.637.41.0022.137210.6860.3951.078100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C22

3c22


Resolution: 1.6→19.94 Å / SU ML: 0.1848 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2134 3921 5.25 %
Rwork0.1825 70761 -
obs0.1841 74682 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.73 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4278 0 132 660 5070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644666
X-RAY DIFFRACTIONf_angle_d0.87786365
X-RAY DIFFRACTIONf_chiral_restr0.0557625
X-RAY DIFFRACTIONf_plane_restr0.0051806
X-RAY DIFFRACTIONf_dihedral_angle_d17.58461721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.28393920.26447035X-RAY DIFFRACTION99.97
1.66-1.720.26943580.23897073X-RAY DIFFRACTION99.97
1.72-1.80.27453630.23017110X-RAY DIFFRACTION99.97
1.8-1.90.26783880.22257025X-RAY DIFFRACTION100
1.9-2.020.24964620.21427011X-RAY DIFFRACTION99.97
2.02-2.170.23764110.2027052X-RAY DIFFRACTION100
2.17-2.390.23753550.19447079X-RAY DIFFRACTION99.99
2.39-2.730.23453970.18717118X-RAY DIFFRACTION100
2.73-3.440.19963870.1687101X-RAY DIFFRACTION100
3.44-19.940.16044080.14437157X-RAY DIFFRACTION99.92

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