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- PDB-5ffr: Crystal Structure of Surfactant Protein-A complexed with phosphoc... -

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Basic information

Entry
Database: PDB / ID: 5ffr
TitleCrystal Structure of Surfactant Protein-A complexed with phosphocholine
ComponentsPulmonary surfactant-associated protein A
KeywordsSUGAR BINDING PROTEIN / COLLECTIN / CARBOHYDRATE BINDING / LECTIN / LIPID BINDING
Function / homology
Function and homology information


Signal regulatory protein family interactions / Surfactant metabolism / Toll Like Receptor 4 (TLR4) Cascade / 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 ...Signal regulatory protein family interactions / Surfactant metabolism / Toll Like Receptor 4 (TLR4) Cascade / 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 / response to retinoic acid / response to glucocorticoid / positive regulation of phagocytosis / 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) ...: / 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
PHOSPHOCHOLINE / Pulmonary surfactant-associated protein A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsGoh, B.C. / Wu, H. / Rynkiewicz, M.J. / Schulten, K. / Seaton, B.A. / McCormack, F.X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)PO1AI0833222 United States
CitationJournal: Biochemistry / Year: 2016
Title: Elucidation of Lipid Binding Sites on Lung Surfactant Protein A Using X-ray Crystallography, Mutagenesis, and Molecular Dynamics Simulations.
Authors: Goh, B.C. / Wu, H. / Rynkiewicz, M.J. / Schulten, K. / Seaton, B.A. / McCormack, F.X.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)16,9524
Polymers16,7051
Non-polymers2473
Water1,72996
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)50,85512
Polymers50,1143
Non-polymers7429
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 area5190 Å2
ΔGint-115 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.349, 97.349, 44.645
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 16704.580 Da / Num. of mol.: 1 / Fragment: neck and carbohydrate recognition domain / Mutation: N187S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sftpa1, Sftp-1, Sftp1, Sftpa / Plasmid: PVL 1392 / Production host: Trichoplusia ni (cabbage looper) / 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-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.66 Å3/Da / Density % sol: 66.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Crystals were grown in hanging drops over reservoirs containing 10 mM sodium cacodylate (pH 6.0), 10 mM calcium acetate, and 10% (w/v) PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 12362 / % possible obs: 99.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 41.98 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.689 / Net I/av σ(I): 27.678 / Net I/σ(I): 27.2 / Num. measured all: 57879
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.2840.37412251.61699.7
2.28-2.3740.30512191.63699.8
2.37-2.4840.23312351.6399.7
2.48-2.614.20.18612271.70799.8
2.61-2.774.50.1412391.79799.9
2.77-2.984.90.11312291.93899.8
2.98-3.285.30.09112311.95399.8
3.28-3.755.30.06612601.7599.8
3.75-4.75.30.04912281.51898
4.7-155.20.03612691.33798.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.2→14.34 Å / FOM work R set: 0.8724 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 1197 9.85 %
Rwork0.1693 10957 -
obs0.1718 12154 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.21 Å2 / Biso mean: 33.73 Å2 / Biso min: 11.43 Å2
Refinement stepCycle: final / Resolution: 2.2→14.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 13 96 1228
Biso mean--56.36 36.82 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081161
X-RAY DIFFRACTIONf_angle_d0.7441593
X-RAY DIFFRACTIONf_chiral_restr0.047166
X-RAY DIFFRACTIONf_plane_restr0.003203
X-RAY DIFFRACTIONf_dihedral_angle_d14.187424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1985-2.28620.26061230.21231144126794
2.2862-2.38970.26691290.20341188131795
2.3897-2.51510.24441280.19461198132698
2.5151-2.67170.22741310.18781215134698
2.6717-2.87650.22111350.18061229136499
2.8765-3.16320.19621390.1861233137299
3.1632-3.61450.19441360.165112401376100
3.6145-4.52990.15191350.14851238137398
4.5299-14.33990.18671410.15961272141399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7910.33070.68712.93252.74368.71210.00270.59430.2705-0.8188-0.11980.0878-0.92480.00260.28320.34990.07160.02180.25880.03720.20645.271533.369425.6624
25.4533.28061.2982.97310.85862.67690.36190.082-0.75360.314-0.014-0.51890.20970.4938-0.15210.13370.0094-0.05370.275-0.01570.239871.874733.002240.5599
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 87 through 109 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 228 )A0

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