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- PDB-6f03: The crystal structure of secreted antigen BPSL2520 -

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Basic information

Entry
Database: PDB / ID: 6f03
TitleThe crystal structure of secreted antigen BPSL2520
ComponentsBPSL2520
KeywordsIMMUNE SYSTEM / Antigen / Burkholderia / putative exported protein
Function / homologyDomain of unknown function DUF2059 / Uncharacterized protein conserved in bacteria (DUF2059) / ACETATE ION / Putative exported protein
Function and homology information
Biological speciesBurkholderia pseudomallei K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsGourlay, L.J.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione Cariplo2009-3577 Italy
CitationJournal: To Be Published
Title: The crystal structure of secreted antigen BPSL2520
Authors: Gourlay, L.J.
History
DepositionNov 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BPSL2520
B: BPSL2520
C: BPSL2520
D: BPSL2520
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,36311
Polymers86,9024
Non-polymers4607
Water1,53185
1
A: BPSL2520
B: BPSL2520
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8208
Polymers43,4512
Non-polymers3686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-61 kcal/mol
Surface area18890 Å2
MethodPISA
2
C: BPSL2520
D: BPSL2520
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5433
Polymers43,4512
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-51 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.955, 52.731, 136.122
Angle α, β, γ (deg.)90.00, 93.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BPSL2520


Mass: 21725.615 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria)
Gene: BPSL2520 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q63S01
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30 % PEG 4000, 0.2 M ammonium acetate, 0.1M HEPES pH 7.0. 20% glycerol added for cryoprotection

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 240723 / Num. obs: 36157 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 35764 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155-0000)refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→38.954 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1814 5.03 %
Rwork0.2024 --
obs0.2045 36071 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→38.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4871 0 29 85 4985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084991
X-RAY DIFFRACTIONf_angle_d0.8616749
X-RAY DIFFRACTIONf_dihedral_angle_d10.7343132
X-RAY DIFFRACTIONf_chiral_restr0.046782
X-RAY DIFFRACTIONf_plane_restr0.006887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25950.31431390.2592585X-RAY DIFFRACTION100
2.2595-2.3260.27841340.23382600X-RAY DIFFRACTION100
2.326-2.40110.27631410.23152647X-RAY DIFFRACTION100
2.4011-2.48690.2731250.2272640X-RAY DIFFRACTION100
2.4869-2.58640.29951420.23892577X-RAY DIFFRACTION100
2.5864-2.70410.32461350.23352626X-RAY DIFFRACTION99
2.7041-2.84660.24821390.22732630X-RAY DIFFRACTION100
2.8466-3.02490.30291420.21812649X-RAY DIFFRACTION100
3.0249-3.25840.2331390.2212629X-RAY DIFFRACTION100
3.2584-3.58610.25581410.20062640X-RAY DIFFRACTION99
3.5861-4.10450.23191440.17792662X-RAY DIFFRACTION100
4.1045-5.16930.20391440.16762650X-RAY DIFFRACTION99
5.1693-38.96040.19871490.18222722X-RAY DIFFRACTION99
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)
10.9275-0.1057-0.66350.7585-0.35570.54450.0806-0.07230.06030.04560.0996-0.07490.04380.12830.00370.1596-0.022-0.00320.1966-0.00460.2626-19.98622.368990.4819
20.5034-0.2436-0.57250.37810.15480.42060.0558-0.04980.12230.18040.0708-0.0578-0.09450.060100.244-0.021-0.03050.1745-0.01530.2676-19.37651.952589.1919
3-0.1829-0.38980.21320.01080.15130.02450.1026-0.1636-0.09510.2183-0.0018-0.03160.604-0.24270.0040.2885-0.0244-0.01180.299-0.00190.22365.4553.546295.8283
40.1090.11590.68510.298-0.08330.86410.0111-0.0439-0.02090.05460.0884-0.0152-0.09920.00030.00020.24040.0263-0.01740.2498-0.00970.25726.62287.855293.1453
5-0.1886-0.1033-0.2111-0.1161-0.24180.19140.112-0.19450.03010.298-0.1004-0.1633-0.22980.19410.00050.3581-0.03910.03190.3376-0.02880.2816-19.21766.676592.8646
60.3997-0.0388-0.85520.4751-0.29720.8302-0.02470.0854-0.0418-0.17520.05510.13770.6558-0.0410.00340.4164-0.0155-0.03520.34450.0030.296716.15121.301929.0947
7-0.1465-0.2430.1706-0.2851-0.09210.07560.03370.0755-0.0215-0.06830.0213-0.06880.06420.022800.3943-0.0182-0.00710.2980.03140.2382-6.13493.589135.6791
8-0.21610.11030.78980.13460.29221.10140.00830.05040.0783-0.06230.04270.0225-0.44440.07330.00010.4494-0.009-0.01760.39990.03580.3224-11.57678.206425.5009
90.5153-0.3547-0.0116-0.23470.16160.28910.08280.0580.0072-0.1074-0.00790.0502-0.00880.0870.0180.4225-0.00330.03030.2786-0.00350.25788.07926.255636.9618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 194 )
4X-RAY DIFFRACTION4chain 'B' and (resid 34 through 150 )
5X-RAY DIFFRACTION5chain 'B' and (resid 151 through 196 )
6X-RAY DIFFRACTION6chain 'C' and (resid 36 through 135 )
7X-RAY DIFFRACTION7chain 'C' and (resid 136 through 194 )
8X-RAY DIFFRACTION8chain 'D' and (resid 36 through 135 )
9X-RAY DIFFRACTION9chain 'D' and (resid 136 through 195 )

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