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- PDB-7ui2: The crystal structure of 15kDa Phlebotomus papatasi salivary prot... -

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Basic information

Entry
Database: PDB / ID: 7ui2
TitleThe crystal structure of 15kDa Phlebotomus papatasi salivary protein Ppsp15.
ComponentsSP15 protein
KeywordsPROTEIN BINDING / SALIVARY / SANDFLY / VACCINE / LEISHMANIA
Function / homologyPheromone/general odorant binding protein superfamily / odorant binding / extracellular region / ACETATE ION / SP15 protein
Function and homology information
Biological speciesPhlebotomus papatasi (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The crystal structure of 15kDa Phlebotomus papatasi salivary protein Ppsp15.
Authors: Tolbert, W.D. / Pazgier, M.
History
DepositionMar 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SP15 protein
B: SP15 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4083
Polymers30,3492
Non-polymers591
Water6,323351
1
A: SP15 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2342
Polymers15,1751
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SP15 protein


Theoretical massNumber of molelcules
Total (without water)15,1751
Polymers15,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.380, 54.610, 61.620
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SP15 protein


Mass: 15174.511 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phlebotomus papatasi (insect) / Production host: Komagataella pastoris (fungus) / References: UniProt: F8R290
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350 0.2 M sodium chloride 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. obs: 128818 / % possible obs: 96.2 % / Redundancy: 3.3 % / CC1/2: 0.976 / Rpim(I) all: 0.066 / Rsym value: 0.103 / Net I/σ(I): 2.4
Reflection shellResolution: 1.19→1.26 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 9811 / CC1/2: 0.423 / Rpim(I) all: 0.484 / Rsym value: 0.75 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OZD

4ozd


Resolution: 1.19→40.87 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.49 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.227 6931 5.38 %
Rwork0.2116 --
obs0.2133 128818 90.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.19→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 4 351 2440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052146
X-RAY DIFFRACTIONf_angle_d0.8552879
X-RAY DIFFRACTIONf_dihedral_angle_d4.762285
X-RAY DIFFRACTIONf_chiral_restr0.082303
X-RAY DIFFRACTIONf_plane_restr0.006371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.220.3473070.37745954X-RAY DIFFRACTION84
1.22-1.240.37323110.36125906X-RAY DIFFRACTION83
1.24-1.260.36083330.34775921X-RAY DIFFRACTION84
1.26-1.290.2932660.32795956X-RAY DIFFRACTION83
1.29-1.320.30022510.30435697X-RAY DIFFRACTION81
1.32-1.350.25612940.2836121X-RAY DIFFRACTION87
1.35-1.380.31323460.28126086X-RAY DIFFRACTION85
1.38-1.420.32822930.27536181X-RAY DIFFRACTION87
1.42-1.460.2713310.26015997X-RAY DIFFRACTION85
1.46-1.510.2952890.25515902X-RAY DIFFRACTION82
1.51-1.560.24433370.22826023X-RAY DIFFRACTION85
1.56-1.620.21683040.22516304X-RAY DIFFRACTION88
1.62-1.70.24233780.21846165X-RAY DIFFRACTION88
1.7-1.790.26543450.23426328X-RAY DIFFRACTION88
1.79-1.90.22323220.22485884X-RAY DIFFRACTION83
1.9-2.040.22853150.21236476X-RAY DIFFRACTION91
2.04-2.250.2433140.20066431X-RAY DIFFRACTION91
2.25-2.570.20213410.18986394X-RAY DIFFRACTION89
2.57-3.240.18483300.17366301X-RAY DIFFRACTION89
3.24-40.870.1954090.16236375X-RAY DIFFRACTION90
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)
12.66520.5774-0.50932.5893-0.19471.9971-0.1050.00070.0324-0.0064-0.0127-0.01550.1778-0.14380.04950.1048-0.01190.00480.07130.00950.0488-13.1317-9.895-18.6437
22.1015-0.29640.46732.35-0.07312.0387-0.1-0.14420.057-0.06090.10990.0075-0.0469-0.04240.04280.0571-0.02270.00870.04960.00260.058-30.6306-32.6232-12.2482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid -1 through 122)
2X-RAY DIFFRACTION2(chain 'B' and resid -4 through 122)

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