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- PDB-1g5z: CRYSTAL STRUCTURE OF LYME DISEASE ANTIGEN OUTER SURFACE PROTEIN C... -

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Basic information

Entry
Database: PDB / ID: 1g5z
TitleCRYSTAL STRUCTURE OF LYME DISEASE ANTIGEN OUTER SURFACE PROTEIN C (OSPC) FROM BORRELIA BURGDORFERI STRAIN N40
ComponentsOUTER SURFACE PROTEIN C
KeywordsIMMUNE SYSTEM / Surface Protein / Alpha helix protein
Function / homologyLipoprotein, type 6 / Lipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / Four Helix Bundle (Hemerythrin (Met), subunit A) / cell outer membrane / Up-down Bundle / Mainly Alpha / Outer surface protein C
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsEicken, C. / Sharma, V. / Klabunde, T. / Owens, R.T. / Pikas, D.S. / Hook, M. / Sacchettini, J.C.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of Lyme disease antigen outer surface protein C from Borrelia burgdorferi.
Authors: Eicken, C. / Sharma, V. / Klabunde, T. / Owens, R.T. / Pikas, D.S. / Hook, M. / Sacchettini, J.C.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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

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Assembly

Deposited unit
A: OUTER SURFACE PROTEIN C


Theoretical massNumber of molelcules
Total (without water)17,6921
Polymers17,6921
Non-polymers00
Water3,477193
1
A: OUTER SURFACE PROTEIN C

A: OUTER SURFACE PROTEIN C


Theoretical massNumber of molelcules
Total (without water)35,3842
Polymers35,3842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4150 Å2
ΔGint-34 kcal/mol
Surface area15040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)32.079, 47.052, 110.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

21A-599-

HOH

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Components

#1: Protein OUTER SURFACE PROTEIN C


Mass: 17692.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Production host: Escherichia coli (E. coli) / References: UniProt: O31117
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1500, EDTA, DTT, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
210 mMTris-HCl1reservoir
35 mMdithiothreitol1reservoir
412 %PEG15001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54078 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 23, 1999 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54078 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 5757 / Num. obs: 5757 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Redundancy: 3.9 % / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.067 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.7 % / Rsym value: 0.207 / % possible all: 89.6
Reflection
*PLUS
Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 89.6 % / Rmerge(I) obs: 0.207

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→19.14 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 253477.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 315 5.6 %RANDOM
Rwork0.196 ---
obs0.196 5581 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.83 Å20 Å20 Å2
2---7.58 Å20 Å2
3---0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.51→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 0 193 1433
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it1.452
X-RAY DIFFRACTIONc_scangle_it2.172.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 50 6.6 %
Rwork0.251 708 -
obs--75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. reflection obs: 5261 / Rfactor Rfree: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

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