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- PDB-3q6p: Salivary protein from Lutzomyia longipalpis. Selenomethionine der... -

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Basic information

Entry
Database: PDB / ID: 3q6p
TitleSalivary protein from Lutzomyia longipalpis. Selenomethionine derivative
Components43.2 kDa salivary protein
KeywordsPROTEIN BINDING / ligand binding protein / beta propeller / ligand binding
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Major royal jelly protein/protein yellow / Major royal jelly protein / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / 43.2 kDa salivary protein
Similarity search - Component
Biological speciesLutzomyia longipalpis (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.75 Å
AuthorsAndersen, J.F. / Xu, X. / Chang, B.W. / Collin, N. / Valenzuela, J.G. / Ribeiro, J.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and function of a "yellow" protein from saliva of the sand fly Lutzomyia longipalpis that confers protective immunity against Leishmania major infection.
Authors: Xu, X. / Oliveira, F. / Chang, B.W. / Collin, N. / Gomes, R. / Teixeira, C. / Reynoso, D. / My Pham, V. / Elnaiem, D.E. / Kamhawi, S. / Ribeiro, J.M. / Valenzuela, J.G. / Andersen, J.F.
History
DepositionJan 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 43.2 kDa salivary protein
B: 43.2 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4633
Polymers87,2712
Non-polymers1921
Water1,17165
1
A: 43.2 kDa salivary protein


Theoretical massNumber of molelcules
Total (without water)43,6351
Polymers43,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 43.2 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8282
Polymers43,6351
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.355, 120.355, 248.934
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein 43.2 kDa salivary protein


Mass: 43635.426 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lutzomyia longipalpis (insect) / Gene: LJM-11, LJM11_Clu9 / Plasmid: pET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5WPU9
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 10 % PEG 6000, 0.1 M sodium citrate, 6 mM Nickel chloride, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionRedundancy: 12.5 % / Av σ(I) over netI: 51.32 / Number: 653588 / Rmerge(I) obs: 0.094 / Χ2: 2.27 / D res high: 2.75 Å / D res low: 40 Å / Num. obs: 52208 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.454099.710.0352.78511.8
5.927.4510010.0472.87911.5
5.175.9210010.0563.4711.8
4.75.1710010.0593.55211.7
4.364.710010.0593.30412.1
4.114.3610010.0612.85812.4
3.94.1110010.0662.53212.5
3.733.910010.082.40912.6
3.593.7310010.0922.25412.7
3.463.5910010.1042.08612.8
3.363.4610010.1251.89412.8
3.263.3610010.1471.76412.8
3.173.2610010.1841.69812.9
3.13.1710010.2171.6512.9
3.033.110010.2771.71812.9
2.963.0310010.3281.68512.9
2.92.9610010.3781.67112.9
2.852.910010.5031.79412.9
2.82.8510010.5761.81612.9
2.752.810010.7112.03112.9
ReflectionResolution: 2.75→40 Å / Num. obs: 52208 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.75-2.812.90.7111100
2.8-2.8512.90.5761100
2.85-2.912.90.5031100
2.9-2.9612.90.3781100
2.96-3.0312.90.3281100
3.03-3.112.90.2771100
3.1-3.1712.90.2171100
3.17-3.2612.90.1841100
3.26-3.3612.80.1471100
3.36-3.4612.80.1251100
3.46-3.5912.80.1041100
3.59-3.7312.70.0921100
3.73-3.912.60.081100
3.9-4.1112.50.0661100
4.11-4.3612.40.0611100
4.36-4.712.10.0591100
4.7-5.1711.70.0591100
5.17-5.9211.80.0561100
5.92-7.4511.50.0471100
7.45-4011.80.035199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.75→40 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 28.055 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.965 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26107 1425 5.1 %RANDOM
Rwork0.19654 ---
obs0.19972 26785 99.28 %-
all-28420 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.436 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.2 Å20 Å2
2---0.41 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6112 0 13 65 6190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226292
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9598517
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9545760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16323.425292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.886151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9171540
X-RAY DIFFRACTIONr_chiral_restr0.0970.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214850
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.591.53796
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16526132
X-RAY DIFFRACTIONr_scbond_it1.79132496
X-RAY DIFFRACTIONr_scangle_it3.0144.52385
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.755→2.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 104 -
Rwork0.242 1889 -
obs--96.7 %
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)
10.89240.02670.1411.628-0.19010.9037-0.04340.0496-0.0210.22460.1601-0.12350.04160.0826-0.11670.40350.14-0.18380.09-0.05750.215982.990713.254631.8762
20.9034-0.2054-0.17970.73950.20491.3023-0.2286-0.0452-0.0017-0.0575-0.03260.02040.06480.05910.26130.45990.17280.08580.07150.06550.237184.0878-30.764912.0042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 381
2X-RAY DIFFRACTION1A382 - 414
3X-RAY DIFFRACTION2B1 - 381
4X-RAY DIFFRACTION2B382
5X-RAY DIFFRACTION2B383 - 414

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