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- PDB-2os9: crystal structure of the trimeric neck and carbohydrate recogniti... -

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Basic information

Entry
Database: PDB / ID: 2os9
Titlecrystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with myoinositol
ComponentsPulmonary surfactant-associated protein D
KeywordsSUGAR BINDING PROTEIN / Surfactant protein / Carbohydrate recognition domain / trimeric
Function / homology
Function and homology information


Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer / surfactant homeostasis ...Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer / surfactant homeostasis / Signal regulatory protein family interactions / negative regulation of interleukin-2 production / lung alveolus development / macrophage chemotaxis / endocytic vesicle / negative regulation of T cell proliferation / multivesicular body / regulation of cytokine production / receptor-mediated endocytosis / reactive oxygen species metabolic process / positive regulation of phagocytosis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / SARS-CoV-1 activates/modulates innate immune responses / carbohydrate binding / lysosome / defense response to bacterium / innate immune response / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / Collectin, 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 ...Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / Collectin, 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
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsHead, J.F.
CitationJournal: Biochemistry / Year: 2007
Title: Critical Role of Arg/Lys343 in the Species-Dependent Recognition of Phosphatidylinositol by Pulmonary Surfactant Protein D.
Authors: Crouch, E. / McDonald, B. / Smith, K. / Roberts, M. / Mealy, T. / Seaton, B. / Head, J.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pulmonary surfactant-associated protein D
B: Pulmonary surfactant-associated protein D
C: Pulmonary surfactant-associated protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,71815
Polymers51,8173
Non-polymers90112
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-153 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.564, 108.692, 55.774
Angle α, β, γ (deg.)90.00, 91.49, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe single trimer of head and neck domains present in the asymmetric unit is the functional unit.

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Components

#1: Protein Pulmonary surfactant-associated protein D / SP-D / PSP-D / Lung surfactant protein D


Mass: 17272.209 Da / Num. of mol.: 3 / Fragment: head and neck domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD, PSPD, SFTP4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettablue / References: UniProt: P35247
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL


Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
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: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 150mM NaCl, 10mM CaCl2, 12% PEG 8000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2005
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→27.9 Å / Num. all: 72901 / Num. obs: 69027 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 23.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4 / Num. unique all: 6343 / Rsym value: 0.26 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2GGU

2ggu


Resolution: 1.7→27.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.907 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22274 5502 8.2 %RANDOM
Rwork0.19492 ---
obs0.19724 61994 92.97 %-
all-66682 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.37 Å2
2--1.16 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 69 515 4038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223586
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9644859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2595449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14525.965171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53615585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7021512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022723
X-RAY DIFFRACTIONr_nbd_refined0.2050.21746
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2397
X-RAY DIFFRACTIONr_metal_ion_refined0.070.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.230
X-RAY DIFFRACTIONr_mcbond_it0.9721.52288
X-RAY DIFFRACTIONr_mcangle_it1.36623557
X-RAY DIFFRACTIONr_scbond_it2.15131437
X-RAY DIFFRACTIONr_scangle_it3.4254.51302
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 316 -
Rwork0.263 4045 -
obs--81.26 %

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