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- PDB-5ffs: Crystal Structure of Surfactant Protein-A Y164A Mutant -

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Basic information

Entry
Database: PDB / ID: 5ffs
TitleCrystal Structure of Surfactant Protein-A Y164A Mutant
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 / positive regulation of phagocytosis / response to glucocorticoid / multivesicular body / response to hormone / circadian rhythm / cellular response to mechanical stimulus / 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 / Resolution: 1.8 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)16,6692
Polymers16,6281
Non-polymers401
Water2,486138
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)50,0066
Polymers49,8853
Non-polymers1203
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 area4910 Å2
ΔGint-73 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.162, 97.162, 44.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

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Components

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


Mass: 16628.484 Da / Num. of mol.: 1 / Fragment: neck and carbohydrate recognition domain / Mutation: N187S/Y164A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.68 Å3/Da / Density % sol: 66.61 %
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: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→90 Å / Num. obs: 26014 / % possible obs: 96.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 27.12 Å2 / Rmerge(I) obs: 0.027 / Χ2: 1.065 / Net I/av σ(I): 40.621 / Net I/σ(I): 45.2 / Num. measured all: 120336
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.761.80.22819631.46374.1
1.76-1.832.50.18125861.48197.7
1.83-1.914.50.14126921.21100
1.91-2.025.20.126701.109100
2.02-2.145.20.06826931.152100
2.14-2.315.20.0526611.145100
2.31-2.545.30.03826931.10599.9
2.54-2.915.30.0326830.94299.9
2.91-3.665.30.02227000.71899.5
3.662-905.10.0226730.97795.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.8→14.645 Å / FOM work R set: 0.897 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1795 1707 7.65 %
Rwork0.162 20614 -
obs0.1635 22321 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.11 Å2 / Biso mean: 30.7 Å2 / Biso min: 12.59 Å2
Refinement stepCycle: final / Resolution: 1.8→14.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1131 0 1 138 1270
Biso mean--22.37 36.93 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081187
X-RAY DIFFRACTIONf_angle_d1.2261614
X-RAY DIFFRACTIONf_chiral_restr0.077173
X-RAY DIFFRACTIONf_plane_restr0.004213
X-RAY DIFFRACTIONf_dihedral_angle_d14.192439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.8530.23981300.20991635176595
1.853-1.91260.23021420.17121713185598
1.9126-1.98080.21551410.17231706184799
1.9808-2.05990.18721410.16911703184499
2.0599-2.15340.17861450.14421719186499
2.1534-2.26660.18051410.154317181859100
2.2666-2.4080.17371420.164617341876100
2.408-2.5930.22791460.163817371883100
2.593-2.85220.20111450.169617381883100
2.8522-3.26090.17351410.171717381879100
3.2609-4.09350.1951500.15661739188999
4.0935-14.64580.13591430.15391734187797
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)
10.34510.0829-0.16430.06720.03060.22460.00120.04710.1325-0.3214-0.0698-0.0999-0.31260.18850.00430.21460.03640.00960.13570.01040.139845.59533.42525.693
21.44771.04730.40690.83150.36761.0770.1347-0.0144-0.23450.1170.0142-0.12770.12150.19570.17850.10910.0052-0.01940.2028-0.01030.156971.61232.9840.148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 87:109 )A87 - 109
2X-RAY DIFFRACTION2( CHAIN A AND RESID 110:228 )A110 - 228

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