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- PDB-1b08: LUNG SURFACTANT PROTEIN D (SP-D) (FRAGMENT) -

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Basic information

Entry
Database: PDB / ID: 1b08
TitleLUNG SURFACTANT PROTEIN D (SP-D) (FRAGMENT)
ComponentsPROTEIN (LUNG SURFACTANT PROTEIN D)
KeywordsSUGAR BINDING PROTEIN / C-TYPE LECTIN / CRD / SP-D / COLECTIN / ALPHA-HELICAL COILED-COIL / LUNG SURFACTANT
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
Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHakansson, K. / Lim, N.K. / Hoppe, H.-J. / Reid, K.B.M.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of the trimeric alpha-helical coiled-coil and the three lectin domains of human lung surfactant protein D.
Authors: Hakansson, K. / Lim, N.K. / Hoppe, H.J. / Reid, K.B.
History
DepositionNov 18, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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_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_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.ptnr1_auth_asym_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_asym_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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (LUNG SURFACTANT PROTEIN D)
B: PROTEIN (LUNG SURFACTANT PROTEIN D)
C: PROTEIN (LUNG SURFACTANT PROTEIN D)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,52812
Polymers51,1683
Non-polymers3619
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-148 kcal/mol
Surface area20590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.960, 109.720, 56.090
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein PROTEIN (LUNG SURFACTANT PROTEIN D) / SP-D


Mass: 17055.906 Da / Num. of mol.: 3
Fragment: TRIMERIC FRAGMENT CONSISTING OF LECTIN DOMAINS AND ALPHA-HELICAL COILED-COIL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: PULMONARY SURFACTANT / Cellular location: EXTRA-CELLULAR / Organ: LUNG / Plasmid: PPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P35247
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.4 Å3/Da / Density % sol: 63.41 %
Crystal growpH: 7
Details: AN EQUAL AMOUNT OF PROTEIN SOLUTION (8 MG/ML PROTEIN IN 10 MM TRIS 140 MM NACL 1MM CACL2 0.02% (W/V) NAN3 PH 7.5) AND PRECIPITANT BUFFER (10-20% (W/V) PEG 20000 IN 100 MM TRIS PH 6-8) WERE ...Details: AN EQUAL AMOUNT OF PROTEIN SOLUTION (8 MG/ML PROTEIN IN 10 MM TRIS 140 MM NACL 1MM CACL2 0.02% (W/V) NAN3 PH 7.5) AND PRECIPITANT BUFFER (10-20% (W/V) PEG 20000 IN 100 MM TRIS PH 6-8) WERE MIXED AND VAPOR EQUILIBRATED AGAINST THE LATTER., pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1TRIS11
2NACL11
3CACL211
4NAN311
5PEG 2000011
6TRIS11
7PEG 2000012
8TRIS12
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
210 mMTris-HCl1drop
3140 mM1dropNaCl
41 mM1dropCaCl2
50.02 %(w/v)1dropNaN3
610-20 %(w/v)PEG200001reservoir
7100 mMTris-HCl1reservoir
81

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 28571 / % possible obs: 95 % / Redundancy: 2.45 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.29 / % possible all: 90.6
Reflection
*PLUS
% possible obs: 95 % / Num. measured all: 69933
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 90.6 % / Num. unique obs: 2706 / Num. measured obs: 4769 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4VERSION OF AMOREmodel building
X-PLORrefinement
AMoREVERSION FOR CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HUP

1hup


Resolution: 2.3→20 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 -5 %RANDOM
Rwork0.209 ---
obs0.209 28550 95 %-
Displacement parametersBiso mean: 28.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 9 192 3651
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.9
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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