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- PDB-4ozd: Crystal structure of PdSP15a -

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Basic information

Entry
Database: PDB / ID: 4ozd
TitleCrystal structure of PdSP15a
Components14.4 kDa salivary protein
KeywordsPROTEIN BINDING / Salivary / sandfly / vaccine / Leishmania
Function / homology
Function and homology information


suppression of blood coagulation in another organism / odorant binding / molecular sequestering activity / toxin activity / extracellular region
Similarity search - Function
Pheromone/general odorant binding protein domain / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Salivary protein 15a
Similarity search - Component
Biological speciesPhlebotomus duboscqi (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsAndersen, J.F. / Alvarenga, P.H.
CitationJournal: To be published
Title: Protection against cutaneous leishmaniasis in non-human primates by immunization with an insect salivary protein
Authors: Oliveira, F. / Rowton, E. / Gomes, R. / Castrovinci, P.A. / Lawyer, P.G. / Teixeira, C. / Aslan, H. / Kleeman, L. / Meneses, C. / Rowland, T. / Gilmore, D. / Andersen, J. / Alvarenga, P.H. / ...Authors: Oliveira, F. / Rowton, E. / Gomes, R. / Castrovinci, P.A. / Lawyer, P.G. / Teixeira, C. / Aslan, H. / Kleeman, L. / Meneses, C. / Rowland, T. / Gilmore, D. / Andersen, J. / Alvarenga, P.H. / Kamhawi, S. / Valenzuela, J.G.
History
DepositionFeb 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Structure summary
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Mar 21, 2018Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen
Item: _diffrn_detector.pdbx_collection_date / _entity_src_gen.pdbx_host_org_scientific_name ..._diffrn_detector.pdbx_collection_date / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
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: 14.4 kDa salivary protein
B: 14.4 kDa salivary protein
C: 14.4 kDa salivary protein
D: 14.4 kDa salivary protein
E: 14.4 kDa salivary protein
F: 14.4 kDa salivary protein
G: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)101,2747
Polymers101,2747
Non-polymers00
Water27015
1
A: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: 14.4 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.558, 79.730, 232.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
14.4 kDa salivary protein


Mass: 14467.659 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phlebotomus duboscqi (insect) / Gene: M02 / Organ: Salivary Gland / Plasmid: pET-17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q06KA5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10 % PEG 6000, 0.1M MES pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 24313 / % possible obs: 97.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 77.93 Å2 / Rmerge(I) obs: 0.106 / Χ2: 1.738 / Net I/av σ(I): 16.276 / Net I/σ(I): 12.8 / Num. measured all: 128620
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.95-35.50.74911821.50599.7
3-3.065.70.68812481.57799.5
3.06-3.115.70.59911751.54399.7
3.11-3.185.70.47212041.60399
3.18-3.255.60.41712431.74299.2
3.25-3.325.70.33311921.92998.7
3.32-3.415.60.27111982.0398.5
3.41-3.55.60.24612052.15698.4
3.5-3.65.60.18612352.2198.5
3.6-3.725.50.15611852.30297.8
3.72-3.855.40.1412131.90998.1
3.85-45.40.11711981.98397.7
4-4.195.20.09212331.81897.9
4.19-4.415.10.08212071.6398.1
4.41-4.685.10.07512081.55897.3
4.68-5.0450.07112331.52297.2
5.04-5.554.90.07712071.64896.8
5.55-6.354.80.07612151.47295.9
6.35-84.50.06712431.30395.5
8-504.20.0612890.96292.4

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Processing

Software
NameVersionClassification
HKL-3000phasing
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→40.141 Å / FOM work R set: 0.7617 / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 1210 4.99 %Random selection
Rwork0.1999 23041 --
obs0.2031 24251 97.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.03 Å2 / Biso mean: 88.01 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.95→40.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6993 0 0 15 7008
Biso mean----99999 -
Num. residues----840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067138
X-RAY DIFFRACTIONf_angle_d1.0939510
X-RAY DIFFRACTIONf_chiral_restr0.0411007
X-RAY DIFFRACTIONf_plane_restr0.0051183
X-RAY DIFFRACTIONf_dihedral_angle_d15.3392771
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 (%)
2.95-3.06530.32971100.25632444255494
3.0653-3.20470.30541370.25622569270699
3.2047-3.37360.3461390.24392543268299
3.3736-3.58480.30031420.21792554269699
3.5848-3.86140.27511240.19972588271298
3.8614-4.24960.24381220.17922550267298
4.2496-4.86370.23881290.16332594272398
4.8637-6.12420.25631540.19792595274997
6.1242-40.14490.23861530.22604275793
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)
15.34551.8802-5.28141.4928-1.89965.27020.092-0.0883-0.6939-0.15660.7077-0.28480.56930.8704-1.12240.69820.1072-0.08040.699-0.08340.6239-1.88115.2111-45.8694
22.0037-4.734-8.40932.06293.65558.2235-3.3322-0.9390.0771-0.72480.31923.16322.21370.01081.13071.165-0.1956-0.07020.49330.08491.0962-6.4706-5.1639-50.542
35.04020.9411-4.49226.0136-0.27634.06010.086-0.0689-0.5687-0.0398-0.03060.0023-0.25780.3816-0.09390.34830.0082-0.03790.3366-0.06060.4379-14.63666.6572-47.4968
48.51272.1991-1.91295.00962.08832.47960.7070.77281.90481.5610.4022.0798-0.45210.1893-1.28840.72810.08710.29170.64230.00211.0425-18.013820.0637-47.9411
55.77931.9469-0.46768.5148-2.15745.4758-0.19160.84330.7341-0.86340.48310.4007-0.6429-0.7943-0.36560.6920.11960.14530.5807-0.04190.4946-24.715613.4428-54.3368
67.78215.9814-4.84185.4988-4.01083.8226-0.02330.22950.38640.43540.71781.43570.6704-1.0531-0.47880.52040.13760.05830.4012-0.07570.4801-18.58267.68-57.4728
79.4903-3.18086.18834.3084-3.36255.26080.53660.6107-0.2518-0.09110.1509-0.3997-0.52121.0131-0.31450.7303-0.0120.04930.4733-0.13430.4777-7.902317.6793-54.4674
82.04570.37650.44872.2596-0.09427.9481-0.20380.0059-0.1008-1.05140.00181.0288-0.32931.28140.1620.530.019-0.0720.8951-0.09440.62824.399230.0677-35.9819
96.179-3.53050.5914.3841-0.54738.3690.2988-0.4148-0.5141-0.11460.20620.47510.2685-0.6544-0.36580.3729-0.082-0.06950.46910.08730.44854.754528.3727-31.0598
107.0307-2.0483-5.54958.25922.5237.7863-0.4329-0.4532-0.64790.06040.44070.18441.31790.93270.11620.8016-0.0878-0.13010.4884-0.01910.524712.760217.6282-28.4926
110.5039-1.3199-1.00587.9162-1.5215.67420.7152-0.59040.3653-0.2429-0.37590.24881.30130.1757-0.04020.8514-0.08050.01490.45830.01180.599910.188627.7545-52.1726
124.95220.4590.62169.0248-4.4095.27610.20590.70220.2168-0.8498-0.01360.20590.94650.7315-0.18560.5040.0230.03770.5367-0.10750.41337.23539.584-52.0736
131.60111.05082.25537.5515-1.72834.71560.67540.9091.0565-0.78080.4572.2763-0.0523-1.5002-0.8490.62410.33930.03760.84170.09850.8396-6.867644.4581-50.3807
142.14552.6012-2.42255.9325-0.49065.9497-0.2043-0.38780.57250.93310.3410.9364-1.0779-0.3174-0.030.62210.16650.09080.5630.01060.71931.494453.0219-44.5403
154.03633.7864-2.17545.5225-4.09885.24390.4056-0.9424-0.16280.7822-0.2759-0.0565-0.98220.2315-0.15560.62830.0719-0.01530.4573-0.090.36037.603945.4906-42.7619
166.73070.0817-2.19454.35593.3013.7233-0.117-0.0633-0.4540.4963-0.3053-0.12852.1417-1.24220.24290.9923-0.10610.07370.67030.14470.5312-4.98632.9719-47.6065
174.7485-4.2916-3.98264.68141.23939.87980.33640.7833-0.1828-0.46860.18140.0643-1.3488-0.1018-0.27561.0547-0.1354-0.12930.6767-0.17670.7208-18.368913.8646-29.6293
184.18791.5987-1.02137.2265-0.64936.60940.23880.58840.46350.1056-0.22810.07590.37710.73290.27970.4352-0.0753-0.0670.7106-0.10150.4931-17.51295.5372-32.7781
198.4975-3.89481.71554.8806-4.19194.0887-0.5963-1.20430.21461.16550.74020.9413-0.3083-1.2464-0.4220.6695-0.0580.1530.6464-0.14990.658-33.3721.1088-30.933
206.3775-5.6361-0.89517.07940.73445.560.62042.0473-0.1839-0.6626-0.64921.03711.3149-1.20140.18230.8974-0.26230.07270.7922-0.02580.7008-33.7782-8.3851-37.6365
214.9657-4.11224.09176.4627-7.64679.3307-0.46390.44480.8834-2.27790.2483-2.43680.781.67270.00321.2108-0.2310.27820.5914-0.15330.643-17.5283-11.9635-33.871
224.9351-5.4794.86096.1284-5.49064.9321.1527-0.07830.8776-0.719-0.2897-0.18780.9280.3517-0.35360.5551-0.18840.14460.6149-0.03710.5263-24.8181-2.3224-40.4044
236.87142.42981.43217.91773.32896.82330.07980.24990.7475-0.8340.21390.3447-0.8051-0.5049-0.39880.78830.01350.11680.6865-0.08160.6093-32.217810.501-37.6903
247.38053.27184.28797.0503-0.26073.4279-1.18161.45890.1638-1.61961.3364-0.7869-1.68591.08740.12421.1492-0.35090.0750.9581-0.03330.9373-36.089445.0837-19.8362
253.45172.16152.17572.82673.78845.8587-0.06410.68310.14070.10.6644-0.3381-0.54920.4512-0.46810.5025-0.11590.02870.5448-0.02870.3805-39.729133.3186-19.2491
264.9874.14185.49265.14932.34089.30510.06791.2685-1.2646-1.37660.9922-0.87660.28981.5284-1.491.00340.3189-0.09751.1994-0.33240.8361-29.384922.3459-17.0596
273.71181.13040.67163.24370.12716.43840.1245-1.1299-0.52440.90830.6014-0.2920.8957-0.2268-0.86350.7899-0.048-0.10350.5323-0.10420.5932-42.911723.761-11.0717
287.00490.49182.04425.35381.88775.68140.3659-1.31460.06070.31170.2668-1.3620.34034.4418-0.90511.2354-0.0572-0.00231.3706-0.50590.905-27.539529.0826-8.5079
296.25327.721-1.79342.0068-1.3211.0239-0.3030.04540.3926-0.6201-2.8265-0.6598-0.46292.9791.38141.3744-0.16760.14122.0522-0.27610.9983-26.076336.2314-23.9387
305.3359-0.0045-0.41286.49492.79076.3934-0.35510.0728-0.1066-0.2241-0.33970.3763-0.7787-0.94040.45310.9430.00270.12890.7489-0.07670.5375-24.6191-0.5115-14.6589
316.4883-0.22392.9061.40031.14033.10750.285-0.1087-1.2020.17080.2191-0.05311.6131-0.3709-0.36051.5349-0.11650.01810.56570.0810.7885-16.4795-18.457-16.6283
329.38641.7931-0.11233.18130.22684.98460.09580.23280.0716-0.07850.03670.46981.5185-0.47390.10130.9902-0.1429-0.01290.49310.1140.4945-21.3395-11.469-20.7019
339.5139-1.7023-2.55371.73083.11355.5231-0.7573-0.38810.2196-0.1950.70450.85141.0783-1.1835-0.96411.34-0.37350.27260.7714-0.05131.1065-18.7843-12.80065.2516
342.0606-1.5270.63693.76553.65436.68050.2229-0.74610.5396-1.5271-0.22090.45510.3872-0.93440.28541.1333-0.874-0.23241.2694-0.23860.4649-25.0369-3.89310.1547
354.23272.26560.64374.46250.83883.56750.5707-0.81120.35580.2488-0.36490.4801-0.0686-0.2673-0.22770.83610.15650.1130.6080.00750.4638-9.1014-4.15413.0987
364.720.3454-0.34776.93444.00548.58110.35850.3861-1.64790.39811.5908-2.12761.6721.5646-1.9111.22990.3703-0.20761.0386-0.27750.9864.0411-11.68571.6175
376.2883-0.7172-1.13661.6857-1.73216.40311.08120.77250.3763-0.7305-0.3682-0.8167-0.1182.0994-0.38670.91580.11960.08370.9316-0.13390.64365.0753-0.3501-4.404
387.8151-4.4095-2.89134.43115.297.50520.62570.6536-0.5628-2.1408-0.68510.8452-1.1768-0.2881-0.23810.74040.068-0.02730.6569-0.15290.5297-4.7172-0.4949-6.3312
398.93085.5092-6.33347.6206-4.93634.679-0.69790.4422-0.8302-0.19620.1549-0.53030.1535-0.82840.67741.291-0.0144-0.23410.68020.0930.6773-5.9471-17.8878-0.8316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 17 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 39 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 52 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 87 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 88 through 100 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 122 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 17 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 100 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 122 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 17 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 18 through 39 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 40 through 57 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 58 through 81 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 82 through 105 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 106 through 122 )C0
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 10 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 11 through 29 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 30 through 57 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 58 through 81 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 82 through 87 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 88 through 100 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 101 through 122 )D0
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 17 )E0
25X-RAY DIFFRACTION25chain 'E' and (resid 18 through 39 )E0
26X-RAY DIFFRACTION26chain 'E' and (resid 40 through 57 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 58 through 99 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 100 through 116 )E0
29X-RAY DIFFRACTION29chain 'E' and (resid 117 through 122 )E0
30X-RAY DIFFRACTION30chain 'F' and (resid 1 through 29 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 30 through 81 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 82 through 122 )F0
33X-RAY DIFFRACTION33chain 'G' and (resid 1 through 10 )G0
34X-RAY DIFFRACTION34chain 'G' and (resid 11 through 17 )G0
35X-RAY DIFFRACTION35chain 'G' and (resid 18 through 39 )G0
36X-RAY DIFFRACTION36chain 'G' and (resid 40 through 57 )G0
37X-RAY DIFFRACTION37chain 'G' and (resid 58 through 81 )G0
38X-RAY DIFFRACTION38chain 'G' and (resid 82 through 105 )G0
39X-RAY DIFFRACTION39chain 'G' and (resid 106 through 122 )G0

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