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- PDB-4wrc: Crystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175... -

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Basic information

Entry
Database: PDB / ID: 4wrc
TitleCrystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175E/R197N/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 / response to hormone / multivesicular body / cellular response to nitric oxide / positive regulation of phagocytosis / response to glucocorticoid / 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
HEXANE-1,6-DIOL / Pulmonary surfactant-associated protein A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 / 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 1.3Sep 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 16, 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)16,8675
Polymers16,6331
Non-polymers2344
Water1,49583
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)50,60115
Polymers49,9003
Non-polymers70112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area6450 Å2
ΔGint-128 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.774, 68.774, 168.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 16633.369 Da / Num. of mol.: 1 / Mutation: E171D/P175E/N187S/R197N/K203D
Source method: isolated from a genetically manipulated source
Details: neck and carbohydrate recognition domain / 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-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: DEDN (17 mg/ml) crystallized in hanging drops from a reservoir solution of 0.2 M calcium chloride and 14% (w/v) PEG 3,350. Before freezing, crystals were soaked in reservoir solution ...Details: DEDN (17 mg/ml) crystallized in hanging drops from a reservoir solution of 0.2 M calcium chloride and 14% (w/v) PEG 3,350. Before freezing, crystals were soaked in reservoir solution supplemented with 1.5 M 1,6-hexanediol as a cryoprotectant

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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: Jan 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 14534 / % possible obs: 99.4 % / Redundancy: 10.7 % / Biso Wilson estimate: 32.26 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.65 / Net I/av σ(I): 39.492 / Net I/σ(I): 27.1 / Num. measured all: 155412
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.869.10.47314511.56699.9
1.86-1.9410.80.34314141.574100
1.94-2.0311.10.24914741.638100
2.03-2.1311.10.18114231.686100
2.13-2.2711.20.1414291.738100
2.27-2.4411.20.11114721.72399.9
2.44-2.6911.20.08814481.701100
2.69-3.0711.10.0714641.68499.8
3.07-3.8610.50.05314791.57199.1
3.862-159.60.04414801.58695.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 3PAK

3pak


Resolution: 1.8→13.644 Å / FOM work R set: 0.8326 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 1431 9.96 %
Rwork0.2051 12937 -
obs0.2088 14368 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.71 Å2 / Biso mean: 32.45 Å2 / Biso min: 11.72 Å2
Refinement stepCycle: final / Resolution: 1.8→13.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 11 83 1191
Biso mean--34.07 34.63 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111139
X-RAY DIFFRACTIONf_angle_d1.2081553
X-RAY DIFFRACTIONf_chiral_restr0.083161
X-RAY DIFFRACTIONf_plane_restr0.004201
X-RAY DIFFRACTIONf_dihedral_angle_d14.131412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7987-1.86280.31521410.26871250139196
1.8628-1.93720.28251370.21991247138498
1.9372-2.02510.25441420.22591311145399
2.0251-2.13150.24211400.20371275141599
2.1315-2.26450.21011430.20091273141699
2.2645-2.43840.28271440.20281310145499
2.4384-2.68210.26351530.21071286143999
2.6821-3.06640.2291430.21613251468100
3.0664-3.84890.24261470.20411328147599
3.8489-13.64460.22991410.19271332147395
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)
12.2381-0.51820.22392.91420.05762.86480.0187-0.6428-0.07560.4963-0.2659-0.68540.0670.12340.15810.2255-0.0211-0.09680.31780.08630.3075.9428-37.874928.7246
22.477-1.2271-0.21783.10530.1722.86650.31930.18160.3113-0.3692-0.2145-0.1236-0.3797-0.4415-0.05040.23490.06420.05810.23130.00950.2047-14.4271-21.588813.076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 89 through 107 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 228 )A0

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