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- PDB-4wr9: Crystal Structure of Surfactant Protein-A DED Mutant (E171D/P175E... -

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Basic information

Entry
Database: PDB / ID: 4wr9
TitleCrystal Structure of Surfactant Protein-A DED Mutant (E171D/P175E/K203D)
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 / response to hyperoxia / response to retinoic acid / positive regulation of phagocytosis / response to glucocorticoid / response to hormone / multivesicular body / cellular response to nitric oxide / 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
Pulmonary surfactant-associated protein A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.301 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
DepositionOct 23, 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 / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)16,7974
Polymers16,6761
Non-polymers1203
Water1,31573
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)50,39012
Polymers50,0293
Non-polymers3619
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 area5330 Å2
ΔGint-144 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.190, 97.190, 44.629
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-413-

HOH

Detailsbiological unit is the same as asym.

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Components

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


Mass: 16676.461 Da / Num. of mol.: 1 / Fragment: neck and carbohydrate recognition domain / Mutation: E171D/P175E/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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: The crystals were grown in hanging drops with 10 mM sodium cacodylate (pH 6.0), 80 mM calcium acetate, 0-10% glycerol, and 4-10% (w/v) PEG 20,000 as the reservoir. Before freezing for x-ray ...Details: The crystals were grown in hanging drops with 10 mM sodium cacodylate (pH 6.0), 80 mM calcium acetate, 0-10% glycerol, and 4-10% (w/v) PEG 20,000 as the reservoir. Before freezing for x-ray data collection, crystals were 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

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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: Oct 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 10829 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 37.92 Å2 / Rmerge(I) obs: 0.069 / Χ2: 1.323 / Net I/av σ(I): 24.816 / Net I/σ(I): 18.3 / Num. measured all: 60818
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.384.80.46510891.43199.9
2.38-2.485.20.37110851.41499.9
2.48-2.595.50.29910621.379100
2.59-2.725.60.21810541.25100
2.72-2.895.80.15710881.33899.9
2.89-3.125.90.11410801.285100
3.12-3.435.90.08110741.34599.9
3.43-3.915.90.05910821.302100
3.91-4.95.90.03710941.27599.5
4.9-155.70.03611211.24899.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3pak

3pak


Resolution: 2.301→14.649 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 1075 10.12 %
Rwork0.1652 9544 -
obs0.1689 10619 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.21 Å2 / Biso mean: 49.1631 Å2 / Biso min: 21.44 Å2
Refinement stepCycle: final / Resolution: 2.301→14.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 3 73 1219
Biso mean--73.36 47.52 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131191
X-RAY DIFFRACTIONf_angle_d0.7591595
X-RAY DIFFRACTIONf_chiral_restr0.029168
X-RAY DIFFRACTIONf_plane_restr0.004213
X-RAY DIFFRACTIONf_dihedral_angle_d16.24432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3008-2.40510.28231230.23031143126694
2.4051-2.53130.2451240.19981164128897
2.5313-2.6890.21191300.19641180131097
2.689-2.89510.23021330.18891191132499
2.8951-3.18380.22811340.1781200133499
3.1838-3.63830.20721380.16351207134599
3.6383-4.56080.18511420.14231208135099
4.5608-14.64960.16411510.146112511402100
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)
12.7159-0.02360.71662.99662.04848.8418-0.05840.56940.166-0.697-0.18950.3388-0.6923-0.46140.2260.38210.09180.01120.34060.06080.31544.702132.962623.6666
24.46952.70421.11292.97680.43943.6820.22120.0279-0.58530.1958-0.0359-0.45250.15360.5259-0.18620.21280.0059-0.03460.32620.00330.287271.715932.695440.2273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 84:109A84 - 109
2X-RAY DIFFRACTION2chain A and resid 110:228A110 - 228

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