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- PDB-5n2b: The crystal structure of Burkholderia pseudomallei antigen and ty... -

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Basic information

Entry
Database: PDB / ID: 5n2b
TitleThe crystal structure of Burkholderia pseudomallei antigen and type I fimbria protein BPSL1626.
ComponentsPutative fimbrial subunit type 1
KeywordsIMMUNE SYSTEM / melioidosis / antigen / fimbrial subunit / incomplete immunoglobulin-like fold
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / cell adhesion involved in single-species biofilm formation / Adhesion domain superfamily / pilus / Fimbrial subunit type 1
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGourlay, L.J. / Bolognesi, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione CARIPLO2009-3577 Italy
CitationJournal: Antibodies / Year: 2018
Title: BPSL1626: Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design againstBurkholderia pseudomallei.
Authors: Capelli, R. / Peri, C. / Villa, R. / Nithichanon, A. / Conchillo-Sole, O. / Yero, D. / Gagni, P. / Chiari, M. / Lertmemongkolchai, G. / Cretich, M. / Daura, X. / Bolognesi, M. / Colombo, G. / Gourlay, L.J.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 2, 2019Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative fimbrial subunit type 1
B: Putative fimbrial subunit type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,87813
Polymers37,1952
Non-polymers68311
Water1,76598
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint31 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.866, 102.237, 72.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative fimbrial subunit type 1


Mass: 18597.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: BPSL1626 / Plasmid: pET151-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q63UH6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PACT Premier (Molecular Dimensions) condition I-9 (25% PEG 6000, 0.1M lithium chloride, 0.1M sodium acetate pH 5.0). Solution supplemented with 30% ethylene glycol as cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 27236 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.016 / Net I/σ(I): 31.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3930 / CC1/2: 0.938 / Rpim(I) all: 0.188 / Rsym value: 0.479 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6
RfactorNum. reflection% reflection
Rfree0.2373 1351 4.96 %
Rwork0.2094 --
obs0.2107 27214 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 44 98 2093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022017
X-RAY DIFFRACTIONf_angle_d0.4932737
X-RAY DIFFRACTIONf_dihedral_angle_d7.8611152
X-RAY DIFFRACTIONf_chiral_restr0.045355
X-RAY DIFFRACTIONf_plane_restr0.003346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.34651250.26812574X-RAY DIFFRACTION100
1.9679-2.04670.30251300.24792546X-RAY DIFFRACTION100
2.0467-2.13980.26771530.23392535X-RAY DIFFRACTION100
2.1398-2.25260.25941410.23242549X-RAY DIFFRACTION100
2.2526-2.39370.28641230.22952563X-RAY DIFFRACTION100
2.3937-2.57850.25041340.22372581X-RAY DIFFRACTION100
2.5785-2.83780.25441160.22522606X-RAY DIFFRACTION100
2.8378-3.24820.22841550.21772574X-RAY DIFFRACTION100
3.2482-4.09130.2361300.19532631X-RAY DIFFRACTION100
4.0913-34.17170.19841440.18172704X-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)
12.0382-1.84140.25241.9914-0.38011.32220.19770.15910.33870.1776-0.0028-0.0084-0.094-0.1322-0.13920.25620.0589-0.04660.2333-0.06630.3215-19.4684-6.264614.5412
23.337-1.82682.82312.3972-1.33162.60210.36372.07730.4346-0.2549-0.6142-0.8605-0.33720.82250.2490.37030.0743-0.01880.63570.03760.54448.8064-9.85929.8999
37.70625.10223.60493.41132.71753.11010.2098-0.0906-0.0548-0.2932-0.3613-0.3206-0.19250.18130.14090.30380.0819-0.03530.33450.05340.32836.0588-12.898113.4013
49.64881.75771.62918.75671.85848.0467-0.0189-0.80530.85310.897-0.18721.3083-0.1355-0.49020.21490.39730.10910.06920.43140.06620.4913-23.5301-11.637323.5992
57.37990.3554-2.90223.2763-0.62792.60840.09190.0814-0.1297-0.036-0.05960.43240.2062-0.0805-0.04330.30380.0723-0.08340.2255-0.01180.2296-18.1677-16.345710.4364
64.54770.0622-3.12832.22490.58735.12970.1849-0.2232-0.10540.207-0.00650.3661-0.0550.0116-0.11380.23650.0903-0.02190.31620.05620.2503-14.6994-16.627316.9956
79.4297-1.925-2.62222.97120.86672.95390.07420.2080.5956-0.1206-0.00270.11780.2732-0.011-0.03160.23960.0729-0.05060.21380.05050.1273-12.8497-11.96468.4218
8-0.02140.07150.51460.62780.95972.2977-0.21940.05820.331-0.3115-0.0328-0.5536-0.5695-0.55460.33220.38260.0434-0.0080.4055-0.13020.7522-42.42972.8957-3.8235
91.912.2303-1.42577.1545-1.00053.55850.2135-0.2630.05950.6615-0.303-0.09270.07470.28330.04330.235-0.071-0.05250.3003-0.04210.3077-32.3017-13.1461-6.3445
103.1442.7327-0.91292.4129-1.77935.4990.13930.00790.4704-0.12320.22770.81970.4028-0.3741-0.24090.1979-0.0472-0.02620.2503-0.05730.3411-36.8905-12.407-10.2564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 91 )
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 144 )
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 175 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 57 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 155 )
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 175 )

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