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- PDB-5xts: Crystal structure of the CysR-CTLD3 fragment of human MR at basic... -

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Basic information

Entry
Database: PDB / ID: 5xts
TitleCrystal structure of the CysR-CTLD3 fragment of human MR at basic/neutral pH
ComponentsMacrophage mannose receptor 1
KeywordsSUGAR BINDING PROTEIN / Collagen binding / Lectin-activity / Endocytic receptor / Immune receptor
Function / homology
Function and homology information


cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / virus receptor activity / signaling receptor activity ...cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / virus receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / endosome membrane / cell surface / plasma membrane
Similarity search - Function
Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Ricin-type beta-trefoil lectin domain / C-type lectin, conserved site / C-type lectin domain signature. / Ricin-type beta-trefoil ...Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Ricin-type beta-trefoil lectin domain / C-type lectin, conserved site / C-type lectin domain signature. / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / 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 / Kringle-like fold
Similarity search - Domain/homology
Macrophage mannose receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHe, Y. / Hu, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020102 China
National Natural Science Foundation of China31270772 China
CitationJournal: Structure / Year: 2018
Title: Structural Insights into the pH-Dependent Conformational Change and Collagen Recognition of the Human Mannose Receptor
Authors: Hu, Z. / Shi, X. / Yu, B. / Li, N. / Huang, Y. / He, Y.
History
DepositionJun 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5792
Polymers70,5391
Non-polymers401
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.256, 101.697, 123.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Macrophage mannose receptor 1 / MMR / C-type lectin domain family 13 member D / C-type lectin domain family 13 member D-like / ...MMR / C-type lectin domain family 13 member D / C-type lectin domain family 13 member D-like / Human mannose receptor / hMR / Macrophage mannose receptor 1-like protein 1


Mass: 70539.258 Da / Num. of mol.: 1 / Fragment: UNP residues 22-629
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRC1, CLEC13D, CLEC13DL, MRC1L1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P22897
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% (w/v) polyethylene glycol 20,000, 0.1M imidazole (pH 7.0)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→38.86 Å / Num. obs: 51902 / % possible obs: 99.7 % / Redundancy: 12.8 % / Net I/σ(I): 19.688
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2.214 / Rsym value: 0.713 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data processing
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQO, 5AO5

1dqo

5ao5


Resolution: 2→38.86 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.34
RfactorNum. reflection% reflection
Rfree0.2007 1999 3.85 %
Rwork0.1655 --
obs0.1669 51880 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3700 0 1 557 4258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053814
X-RAY DIFFRACTIONf_angle_d0.7525178
X-RAY DIFFRACTIONf_dihedral_angle_d10.8352252
X-RAY DIFFRACTIONf_chiral_restr0.046530
X-RAY DIFFRACTIONf_plane_restr0.004656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.050.28741380.22893434X-RAY DIFFRACTION98
2.05-2.10540.25621410.19853528X-RAY DIFFRACTION100
2.1054-2.16730.24321400.19013515X-RAY DIFFRACTION100
2.1673-2.23730.20841420.17713522X-RAY DIFFRACTION100
2.2373-2.31720.19431430.16953568X-RAY DIFFRACTION100
2.3172-2.410.22081420.15873539X-RAY DIFFRACTION100
2.41-2.51970.18671410.15633521X-RAY DIFFRACTION100
2.5197-2.65250.19611410.16723526X-RAY DIFFRACTION100
2.6525-2.81860.19171440.16223585X-RAY DIFFRACTION100
2.8186-3.03620.23711430.17083564X-RAY DIFFRACTION100
3.0362-3.34160.20391440.16873589X-RAY DIFFRACTION100
3.3416-3.82470.2091440.16233599X-RAY DIFFRACTION100
3.8247-4.81730.15471460.13463636X-RAY DIFFRACTION100
4.8173-38.8680.20021500.17793755X-RAY DIFFRACTION98

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