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- PDB-4e52: Crystal structure of Haemophilus Eagan 4A polysaccharide bound hu... -

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Entry
Database: PDB / ID: 4.0E+52
TitleCrystal structure of Haemophilus Eagan 4A polysaccharide bound human lung surfactant protein D
ComponentsPulmonary surfactant-associated protein D
KeywordsSUGAR BINDING PROTEIN / Trimeric recombinant collectin fragment / neck+CRD / alpha-helical coiled coil / carbohydrate recognition domain / Lectin
Function / homology
Function and homology information


Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / extracellular matrix structural constituent conferring tensile strength / 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 ...Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / extracellular matrix structural constituent conferring tensile strength / 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 / positive regulation of phagocytosis / regulation of cytokine production / multivesicular body / reactive oxygen species metabolic process / extracellular matrix organization / receptor-mediated endocytosis / SARS-CoV-1 activates/modulates innate immune responses / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / carbohydrate binding / collagen-containing extracellular matrix / 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
Pulmonary surfactant-associated protein D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShrive, A.K. / Greenhough, T.J.
Citation
Journal: Infect.Immun. / Year: 2016
Title: Crystal Structure of a Complex of Surfactant Protein D (SP-D) and Haemophilus influenzae Lipopolysaccharide Reveals Shielding of Core Structures in SP-D-Resistant Strains.
Authors: Clark, H.W. / Mackay, R.M. / Deadman, M.E. / Hood, D.W. / Madsen, J. / Moxon, E.R. / Townsend, J.P. / Reid, K.B. / Ahmed, A. / Shaw, A.J. / Greenhough, T.J. / Shrive, A.K.
#1: Journal: J.Mol.Biol. / Year: 2009
Title: Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325.
Authors: Shrive, A.K. / Martin, C. / Burns, I. / Paterson, J.M. / Martin, J.D. / Townsend, J.P. / Waters, P. / Clark, H.W. / Kishore, U. / Reid, K.B. / Greenhough, T.J.
#2: 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.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _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_asym_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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

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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)57,69014
Polymers56,5053
Non-polymers1,18511
Water9,566531
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-150 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.350, 107.990, 55.650
Angle α, β, γ (deg.)90.000, 92.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pulmonary surfactant-associated protein D / PSP-D / SP-D / Collectin-7 / Lung surfactant protein D


Mass: 18834.957 Da / Num. of mol.: 3 / Fragment: carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFTPD, COLEC7, PSPD, SFTP4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35247
#2: Polysaccharide 4,7-anhydro-3-deoxy-D-manno-oct-2-ulosonic acid-(5-1)-L-glycero-alpha-D-manno-heptopyranose


Type: oligosaccharide / Mass: 412.344 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[AOd1122h_4-7][a11221h-1a_1-5]/1-2/a5-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Araf]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBOTH ENANTIOMERS THAT DIFFER ONLY IN THE CHIRALITY AT ATOM C4 EXIST IN THE STRUCTURE. HOWEVER, THE ...BOTH ENANTIOMERS THAT DIFFER ONLY IN THE CHIRALITY AT ATOM C4 EXIST IN THE STRUCTURE. HOWEVER, THE ENANTIOMERIC SUBSTITUTE OFF C4 ATOM IS NOT VISIBLE IN THE ELECTRON DENSITY MAP.

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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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.7→26.748 Å / Num. obs: 71591 / % possible obs: 99.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.7930.2952.431047104540.29599.9
1.79-1.930.1873.82962198580.187100
1.9-2.0330.1295.22807792830.129100
2.03-2.1930.1045.82624886320.104100
2.19-2.43.10.096.52458080030.09100
2.4-2.693.10.0797.32212571770.079100
2.69-3.13.10.0727.61979463900.072100
3.1-3.83.10.0687.71670453800.068100
3.8-5.383.10.069.21286341740.0699.9
5.38-26.7482.90.0589.3653422400.05896.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.1.4data scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PW9

1pw9


Resolution: 1.7→26.748 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8639 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3624 5.1 %random
Rwork0.1922 ---
obs-71561 99.8 %-
Solvent computationBsol: 40.3212 Å2
Displacement parametersBiso max: 54.44 Å2 / Biso mean: 24.3697 Å2 / Biso min: 11.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.288 Å20 Å2-1.469 Å2
2---2.085 Å20 Å2
3---3.373 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 53 531 4067
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_scbond_it2.0062
X-RAY DIFFRACTIONc_mcangle_it1.6452
X-RAY DIFFRACTIONc_scangle_it2.9952.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.710.3163720.348313491421
1.71-1.720.366680.340913721440
1.72-1.740.3332760.307913511427
1.74-1.750.3003770.286613451422
1.75-1.760.3604720.274213131385
1.76-1.770.2331740.260813851459
1.77-1.790.2914810.260913751456
1.79-1.80.2778660.257613421408
1.8-1.820.2236670.246813331400
1.82-1.830.2678780.239813601438
1.83-1.850.261800.228413491429
1.85-1.860.2338840.23613631447
1.86-1.880.2461610.212313321393
1.88-1.90.2052710.201813861457
1.9-1.910.2505600.205313761436
1.91-1.930.218780.199113461424
1.93-1.950.2362670.197213601427
1.95-1.970.2204740.199913611435
1.97-1.990.2237850.190313371422
1.99-2.020.2432780.195513351413
2.02-2.040.2033600.196514071467
2.04-2.060.2334800.196213541434
2.06-2.090.1762580.183513261384
2.09-2.110.2072690.182513801449
2.11-2.140.2297820.17613771459
2.14-2.170.2163800.182713331413
2.17-2.20.2169840.186913501434
2.2-2.240.246760.191813611437
2.24-2.270.1905650.18613561421
2.27-2.310.2352720.185613731445
2.31-2.350.1954720.180313521424
2.35-2.390.2415610.198413611422
2.39-2.440.2436790.200613701449
2.44-2.490.2021720.187413431415
2.49-2.540.183690.190713781447
2.54-2.60.2144800.199313281408
2.6-2.660.1686750.19313881463
2.66-2.740.2349600.19713561416
2.74-2.820.2252670.192513721439
2.82-2.910.191770.185613781455
2.91-3.010.2306600.195913511411
3.01-3.130.2142790.192213641443
3.13-3.270.216750.194213751450
3.27-3.450.2138670.186413811448
3.45-3.660.1784650.1713661431
3.66-3.950.1695740.16813731447
3.95-4.340.1405690.152513681437
4.34-4.970.1683880.154813551443
4.97-6.260.2607710.210313681439
6.26-500.010.1886690.192913231392
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4cis_peptide.param
X-RAY DIFFRACTION5HK5new_par.txt

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