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- PDB-4wux: Crystal Structure of Surfactant Protein-A DED Mutant (E171D/P175E... -

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Basic information

Entry
Database: PDB / ID: 4wux
TitleCrystal Structure of Surfactant Protein-A DED Mutant (E171D/P175E/K203D) Complexed with Mannose
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 / 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 / response to hyperoxia ...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 / response to hyperoxia / cellular response to nitric oxide / 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
alpha-D-mannopyranose / Pulmonary surfactant-associated protein A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsRynkiewicz, M.J. / Wu, H. / Cafarella, T.R. / Nikolaidis, N.M. / Head, J.F. / 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)#PO1-AI083222 United States
CitationJournal: To be published
Title: Differential ligand binding specificities of the pulmonary collectins are determined by the conformational freedom of a surface loop
Authors: Rynkiewicz, M.J. / Wu, H. / Cafarella, T.R. / Nikolaidis, N.M. / Head, J.F. / Seaton, B.A. / McCormack, F.X.
History
DepositionNov 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pulmonary surfactant-associated protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3456
Polymers16,7241
Non-polymers6215
Water1,38777
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)52,03518
Polymers50,1733
Non-polymers1,86215
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 area8110 Å2
ΔGint-94 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.944, 96.944, 44.994
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-418-

HOH

21A-435-

HOH

31A-436-

HOH

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Components

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


Mass: 16724.461 Da / Num. of mol.: 1 / Fragment: neck and carbohydrate recognition domain / Mutation: E171D/P175E//N187S/K203D
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: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: The crystal was grown in hanging drops using 10 mM sodium cacodylate (pH 6.0), 80 mM calcium acetate, 0-10% glycerol, and 4-10% (w/v) PEG 20,000 as a reservoir. Before freezing for x-ray ...Details: The crystal was grown in hanging drops using 10 mM sodium cacodylate (pH 6.0), 80 mM calcium acetate, 0-10% glycerol, and 4-10% (w/v) PEG 20,000 as a reservoir. Before freezing for x-ray data collection, crystal was soaked in reservoir solution of 10 mM calcium acetate without glycerol, but with stepwise additions of 5, 10, and 15% 2-methyl-2,4-pentanediol with 25% mannose for 10 minutes at each step

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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: Mar 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 18934 / % possible obs: 98.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 35.47 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.257 / Net I/av σ(I): 30.366 / Net I/σ(I): 23.8 / Num. measured all: 98492
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.974.60.50718931.35599.8
1.97-2.055.20.36119221.33999.9
2.05-2.145.30.24819031.334100
2.14-2.255.30.18218931.27100
2.25-2.395.30.13319041.16299.9
2.39-2.585.40.10219051.06999.9
2.58-2.835.40.07519381.1899.8
2.83-3.245.40.05419171.21899.3
3.24-4.075.20.03818521.38695.8
4.07-1550.02818071.29291.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4WR9

4wr9


Resolution: 1.9→14.963 Å / FOM work R set: 0.8841 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 1906 10.07 %
Rwork0.1723 17017 -
obs0.1754 18923 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.7 Å2 / Biso mean: 45.49 Å2 / Biso min: 21.79 Å2
Refinement stepCycle: final / Resolution: 1.9→14.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 38 77 1235
Biso mean--60.66 48.61 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021240
X-RAY DIFFRACTIONf_angle_d1.5391673
X-RAY DIFFRACTIONf_chiral_restr0.06184
X-RAY DIFFRACTIONf_plane_restr0.005218
X-RAY DIFFRACTIONf_dihedral_angle_d14.292469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8995-1.94690.28531380.252112321370100
1.9469-1.99940.22821370.208712081345100
1.9994-2.05810.19521360.183512271363100
2.0581-2.12430.20541360.174712181354100
2.1243-2.20.20471330.160412331366100
2.2-2.28780.18821400.161112251365100
2.2878-2.39160.21191310.15812171348100
2.3916-2.51710.22831420.165112401382100
2.5171-2.6740.2131370.171712311368100
2.674-2.87910.2141350.166712231358100
2.8791-3.16630.20241410.16451224136599
3.1663-3.61880.19041390.16681212135198
3.6188-4.53810.17741230.15521137126090
4.5381-14.96360.20961380.19571190132893
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)
13.3870.76392.45834.87253.47772.00660.04220.434-0.05-0.7832-0.01810.145-0.56450.2346-0.08290.31940.04710.01790.25880.00580.303645.031233.265726.2306
23.1511.64450.6453.16850.34663.29070.10430.1022-0.38850.13580.1071-0.49010.09540.6802-0.21750.20810.0057-0.02170.3868-0.03070.288271.536732.634640.3817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 87:109A87 - 109
2X-RAY DIFFRACTION2chain A and resid 110:228A110 - 228

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