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- PDB-2fkj: The crystal structure of engineered OspA -

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Basic information

Entry
Database: PDB / ID: 2fkj
TitleThe crystal structure of engineered OspA
ComponentsOuter Surface Protein A
KeywordsDE NOVO PROTEIN / BETA SHEET
Function / homology
Function and homology information


cell outer membrane / cell surface / membrane / metal ion binding
Similarity search - Function
C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Beta Barrel ...C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Outer surface protein A / Outer surface protein A
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMakabe, K. / Terechko, V. / Gawlak, G. / Yan, S. / Koide, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Atomic structures of peptide self-assembly mimics.
Authors: Makabe, K. / McElheny, D. / Tereshko, V. / Hilyard, A. / Gawlak, G. / Yan, S. / Koide, A. / Koide, S.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999PROTEIN SEQUENCE IS NOT AVAILABLE IN ANY SEQUENCE DATABASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer Surface Protein A
B: Outer Surface Protein A
C: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)120,6633
Polymers120,6633
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.150, 105.500, 88.981
Angle α, β, γ (deg.)90.00, 93.24, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMonomer in solution

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Components

#1: Protein Outer Surface Protein A


Mass: 40220.953 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Production host: Escherichia coli (E. coli) / References: UniProt: Q45040, UniProt: P0CL66*PLUS

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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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 22% PEG1000, 0.1M Acetate, 0.2M litium sulfate, 3% MPD, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 24305 / Num. obs: 24305 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.17
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 10.19 / Num. unique all: 2426 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.888 / SU B: 57.76 / SU ML: 0.446 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.541 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28162 1161 4.9 %RANDOM
Rwork0.24697 ---
all0.24866 23829 --
obs0.24866 22668 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.512 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å26.75 Å2
2--6.75 Å20 Å2
3----3.86 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8334 0 0 0 8334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228376
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.98811172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56251080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88527.523327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.951151857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5491521
X-RAY DIFFRACTIONr_chiral_restr0.0670.21323
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025811
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.23043
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.231.55343
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.43928631
X-RAY DIFFRACTIONr_scbond_it0.61433033
X-RAY DIFFRACTIONr_scangle_it1.1374.52541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.379 80
Rwork0.377 1670
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)
17.27881.78980.34582.9933-2.36637.3869-0.2109-0.1361-0.1079-0.06550.40430.48950.1966-0.9555-0.1934-0.3812-0.0118-0.0365-0.44690.142-0.19192.2193-11.620471.1637
27.37790.5219-5.90340.1867-0.8036.08120.05090.1002-0.28070.14320.0039-0.31620.0173-0.0196-0.0548-0.2399-0.049-0.0756-0.3315-0.0143-0.168234.34153.789142.7564
35.1604-3.059-4.8566.41593.37676.27950.69120.61140.5129-0.4877-0.5684-0.2543-0.5883-0.5669-0.1229-0.3871-0.0009-0.0784-0.33550.0825-0.21364.6033-2.862615.2044
43.6665-2.9453-0.03956.26411.63414.8902-0.4415-0.4239-0.07150.84960.3670.6357-0.1179-0.00850.0745-0.26270.0118-0.032-0.3599-0.0109-0.1885.268617.788665.9619
51.89880.5723-4.33750.4636-1.164511.5547-0.04980.15520.1503-0.1570.0067-0.0108-0.10030.0270.0431-0.3984-0.1346-0.2466-0.03250.1449-0.296521.055315.476923.5392
612.95093.4754-2.46833.37810.79223.9827-0.23840.087-0.9303-0.27250.0014-0.32620.5324-0.3930.237-0.1631-0.0573-0.0677-0.4737-0.0482-0.26350.644621.6404-5.0535
76.11462.5781-3.211712.4337-3.03945.7606-0.22210.34850.09930.67830.86671.0758-0.0733-1.7968-0.6446-0.4331-0.1665-0.24490.62080.1844-0.3416-7.24770.141347.4408
85.7951-1.0879-4.0940.47371.68125.984-0.08450.3451-0.4599-0.0530.0217-0.07090.5651-0.06910.06270.2296-0.13690.12530.0739-0.0878-0.051328.2093-9.821620.5004
90.6179-1.2227-0.06046.3152-5.01966.7858-0.08580.8003-0.0624-0.7968-0.6609-0.0690.43260.44630.7467-0.076-0.0387-0.13690.9851-0.19440.164745.4388-10.2792-17.5307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA28 - 1416 - 119
2X-RAY DIFFRACTION2AA142 - 269120 - 247
3X-RAY DIFFRACTION3AA270 - 388248 - 366
4X-RAY DIFFRACTION4BB28 - 1416 - 119
5X-RAY DIFFRACTION5BB142 - 269120 - 247
6X-RAY DIFFRACTION6BB270 - 388248 - 366
7X-RAY DIFFRACTION7CC28 - 1416 - 119
8X-RAY DIFFRACTION8CC142 - 269120 - 247
9X-RAY DIFFRACTION9CC270 - 388248 - 366

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