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- PDB-3par: Surfactant Protein-A neck and carbohydrate recognition domain (NC... -

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Basic information

Entry
Database: PDB / ID: 3par
TitleSurfactant Protein-A neck and carbohydrate recognition domain (NCRD) in the absence of ligand
ComponentsPulmonary surfactant-associated protein A
KeywordsSUGAR BINDING PROTEIN / collectin / carbohydrate binding / lectin / mannose
Function / homology
Function and homology information


Signal regulatory protein family interactions / Surfactant metabolism / Regulation of TLR by endogenous ligand / opsonization / response to interleukin-6 / respiratory gaseous exchange by respiratory system / collagen trimer / response to epidermal growth factor / response to vitamin A / cellular response to nitric oxide ...Signal regulatory protein family interactions / Surfactant metabolism / Regulation of TLR by endogenous ligand / opsonization / response to interleukin-6 / respiratory gaseous exchange by respiratory system / collagen trimer / response to epidermal growth factor / response to vitamin A / cellular response to nitric oxide / response to hyperoxia / positive regulation of phagocytosis / response to retinoic acid / response to glucocorticoid / multivesicular body / response to hormone / cellular response to mechanical stimulus / circadian rhythm / carbohydrate binding / response to lipopolysaccharide / response to hypoxia / extracellular space / metal ion binding
Similarity search - Function
Collectin, C-type lectin-like domain / 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 ...Collectin, C-type lectin-like domain / 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 A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsShang, F. / Rynkiewicz, M.J. / McCormack, F.X. / Wu, H. / Cafarella, T.M. / Head, J. / Seaton, B.A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystallographic complexes of surfactant protein A and carbohydrates reveal ligand-induced conformational change.
Authors: Shang, F. / Rynkiewicz, M.J. / McCormack, F.X. / Wu, H. / Cafarella, T.M. / Head, J.F. / Seaton, B.A.
History
DepositionOct 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9054
Polymers16,6731
Non-polymers2323
Water72140
1
A: Pulmonary surfactant-associated protein A
hetero molecules

A: Pulmonary surfactant-associated protein A
hetero molecules

A: Pulmonary surfactant-associated protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,71412
Polymers50,0183
Non-polymers6979
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5650 Å2
ΔGint-141 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.351, 98.351, 44.744
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 16672.580 Da / Num. of mol.: 1 / Fragment: UNP residues 101-248 / Mutation: N187S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sftp-1, Sftp1, Sftpa, Sftpa1 / Plasmid: PVL 1392 / Production host: TRICHOPLUSIA (butterflies/moths) / References: UniProt: P08427
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.75 Å3/Da / Density % sol: 67.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 ul of SP-A (10 mg/ml) was mixed with 1 ul reservoir (50 mM sodium cacodylate (pH = 6.5), 1.2-1.6 M lithium sulfate, and 10 mM calcium chloride). After crystals had grown, the drop was ...Details: 1 ul of SP-A (10 mg/ml) was mixed with 1 ul reservoir (50 mM sodium cacodylate (pH = 6.5), 1.2-1.6 M lithium sulfate, and 10 mM calcium chloride). After crystals had grown, the drop was diluted 1/2 with 50 mM sodium cacodylate (pH = 6.5) and 10 mM calcium chloride. Maltose powder was then added to the drop and dissolved. Prior to data collection, the drop was diluted 1/2 again and more maltose powder was dissolved., VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 10984 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 21.9
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 4.3 / Num. unique all: 683 / % possible all: 91.3

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB CODE 1R13

1r13


Resolution: 2.3→32.19 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 887133.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 867 8 %RANDOM
Rwork0.227 ---
obs0.227 10788 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.4807 Å2 / ksol: 0.353963 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.85 Å29.05 Å20 Å2
2--5.85 Å20 Å2
3----11.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.3→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 11 40 1186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.413 103 6.3 %
Rwork0.345 1532 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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