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

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Basic information

Entry
Database: PDB / ID: 4wrf
TitleCrystal Structure of Surfactant Protein-A DEDN Mutant (E171D/P175E/R197N/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 / 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
HEXANE-1,6-DIOL / alpha-D-mannopyranose / Pulmonary surfactant-associated protein A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.901 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _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
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
Revision 1.5Oct 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)17,0877
Polymers16,6331
Non-polymers4546
Water1,964109
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)51,26221
Polymers49,9003
Non-polymers1,36218
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 area7410 Å2
ΔGint-112 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.157, 69.157, 169.566
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

Detailsbiological unit is the same as asym.

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 16633.369 Da / Num. of mol.: 1 / Fragment: neck and carbohydrate recognition domain / Mutation: E171D/P175E/N187S/R197N/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
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 4 types, 114 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.57 %
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, the 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, the crystals were soaked in reservoir solution supplemented with 1.5 M 1,6-hexanediol as a cryoprotectant with 5% (w/v) mannose for 30 minutes

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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 21, 2013
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: 12478 / % possible obs: 98.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 30.97 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.412 / Net I/av σ(I): 28.08 / Net I/σ(I): 23.2 / Num. measured all: 74138
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.973.60.39711341.0890.1
1.97-2.055.70.29312181.09999.8
2.05-2.146.30.21112501.18199.9
2.14-2.255.80.16312451.35299.9
2.25-2.3960.11712621.351100
2.39-2.586.60.08912571.248100
2.58-2.836.60.07212331.42599.9
2.83-3.246.60.06412771.51699.9
3.24-4.075.70.05512891.79699.2
4.07-156.20.06313131.85698.9

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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 code 4WRC

4wrc


Resolution: 1.901→14.929 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1232 10.06 %
Rwork0.1981 11010 -
obs0.2026 12242 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.52 Å2 / Biso mean: 37.8438 Å2 / Biso min: 20.51 Å2
Refinement stepCycle: final / Resolution: 1.901→14.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 24 109 1247
Biso mean--37.8 44.95 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161183
X-RAY DIFFRACTIONf_angle_d0.9361573
X-RAY DIFFRACTIONf_chiral_restr0.041170
X-RAY DIFFRACTIONf_plane_restr0.004206
X-RAY DIFFRACTIONf_dihedral_angle_d12.743433
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 (%)
1.9007-1.97670.3181170.27281057117485
1.9767-2.06640.28461350.2121186132196
2.0664-2.17510.23841310.1961225135698
2.1751-2.31090.22961320.20331236136898
2.3109-2.48850.22851430.19061214135799
2.4885-2.73760.28271350.19031253138899
2.7376-3.13050.25231400.194512601400100
3.1305-3.93220.23261420.18811262140499
3.9322-14.9290.23311570.2021317147499
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)
11.49230.5537-0.00731.58830.27470.6147-0.0613-0.6423-0.09210.556-0.232-0.2301-0.1488-0.1364-0.03150.31180.0167-0.05130.37690.06180.37435.8887-37.737727.7347
22.3807-0.79740.19753.369-0.33623.91170.09110.06960.0812-0.0854-0.13680.0511-0.1977-0.3102-0.0050.17750.0237-0.00160.2412-0.02460.2002-14.7975-21.689813.1814
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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