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Basic information

Entry
Database: PDB / ID: 1pwb
TitleHigh resolution crystal structure of an active recombinant fragment of human lung surfactant protein D with maltose
ComponentsPulmonary surfactant-associated protein D
KeywordsSIGNALING PROTEIN / collectin / c-type lectin / alpha-helical coiled coil / carbohydrate recognition domain
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 / positive regulation of phagocytosis / negative regulation of T cell proliferation / regulation of cytokine production / reactive oxygen species metabolic process / multivesicular body / receptor-mediated endocytosis / SARS-CoV-1 activates/modulates innate immune responses / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / Lectin C-type domain ...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
alpha-maltose / alpha-D-glucopyranose / Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsShrive, A.K. / Tharia, H.A. / Strong, P. / Kishore, U. / Burns, I. / Rizkallah, P.J. / Reid, K.B. / Greenhough, T.J.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: High-resolution structural insights into ligand binding and immune cell recognition by human lung surfactant protein D
Authors: Shrive, A.K. / Tharia, H.A. / Strong, P. / Kishore, U. / Burns, I. / Rizkallah, P.J. / Reid, K.B. / Greenhough, T.J.
#1: Journal: Structure / 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
DepositionJul 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_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.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)57,56815
Polymers56,5053
Non-polymers1,06312
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-146 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.480, 108.300, 55.780
Angle α, β, γ (deg.)90.00, 91.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18834.957 Da / Num. of mol.: 3 / Fragment: recombinant fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P35247
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 10000, Tris, maltose, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
210 mMTris1drop
3140 mM1dropNaCl
410 mM1dropCaCl2pH7.5
512 %PEG100001reservoir
610 mMTris1reservoir
70.1 Mmaltose1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.244 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2000
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.244 Å / Relative weight: 1
ReflectionResolution: 1.4→32 Å / Num. all: 122387 / Num. obs: 122387 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.043 / Net I/σ(I): 9.2
Reflection shellResolution: 1.4→1.48 Å / Mean I/σ(I) obs: 3 / Num. unique all: 14247 / Rsym value: 0.245 / % possible all: 76
Reflection
*PLUS
Num. measured all: 648490 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 76 % / Num. unique obs: 14247 / Num. measured obs: 55566 / Rmerge(I) obs: 0.245

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLOR3.851refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1b08

1b08


Resolution: 1.4→32.1 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 6162 -random
Rwork0.205 ---
all0.205 122387 --
obs0.205 122387 94.9 %-
Refinement stepCycle: LAST / Resolution: 1.4→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3476 0 56 506 4038
LS refinement shellResolution: 1.4→1.46 Å
RfactorNum. reflection
Rfree0.37 599
Rwork0.36 -
obs-11843
Refinement
*PLUS
Highest resolution: 1.4 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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