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- PDB-1ggq: OUTER SURFACE PROTEIN C (OSPC) OF BORRELIA BURGDORFERI STRAIN B31 -

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Basic information

Entry
Database: PDB / ID: 1ggq
TitleOUTER SURFACE PROTEIN C (OSPC) OF BORRELIA BURGDORFERI STRAIN B31
ComponentsOUTER SURFACE PROTEIN C
KeywordsMEMBRANE PROTEIN / Lyme disease antigen / helical bundle / homodimer
Function / homology
Function and homology information


external side of cell outer membrane / cell surface / membrane
Similarity search - Function
Lipoprotein, type 6 / Lipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Outer surface protein C
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsDunn, J.J. / Lawson, C.L.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of outer surface protein C (OspC) from the Lyme disease spirochete, Borrelia burgdorferi.
Authors: Kumaran, D. / Eswaramoorthy, S. / Luft, B.J. / Koide, S. / Dunn, J.J. / Lawson, C.L. / Swaminathan, S.
History
DepositionSep 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER SURFACE PROTEIN C
B: OUTER SURFACE PROTEIN C
C: OUTER SURFACE PROTEIN C
D: OUTER SURFACE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4145
Polymers74,3894
Non-polymers241
Water2,018112
1
A: OUTER SURFACE PROTEIN C
B: OUTER SURFACE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2193
Polymers37,1952
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-39 kcal/mol
Surface area14220 Å2
MethodPISA
2
C: OUTER SURFACE PROTEIN C
D: OUTER SURFACE PROTEIN C


Theoretical massNumber of molelcules
Total (without water)37,1952
Polymers37,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-39 kcal/mol
Surface area14230 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-85 kcal/mol
Surface area28090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.206, 33.654, 47.993
Angle α, β, γ (deg.)84.04, 81.55, 89.23
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a dimer. There are two dimers in the asymmetric unit, chains A + B and chains C + D

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Components

#1: Protein
OUTER SURFACE PROTEIN C / OSPC


Mass: 18597.352 Da / Num. of mol.: 4 / Fragment: RESIDUES 38-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: B31 / Production host: Escherichia coli (E. coli) / Keywords: NATIVE, UNLIPIDATED FORM / References: UniProt: Q07337
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 23 % (w/v) PEG 3350, 50 mM Tris/HCl pH 8.5, 100 mM MgCl2, 10% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128-30 %PEG335011
280 mMTris-HCl11
3100 mM11MgCl2
418 %glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.092
DetectorType: BRANDEIS / Detector: CCD / Date: Apr 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.092 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 25209 / Num. obs: 25209 / % possible obs: 94.1 % / Observed criterion σ(F): -10 / Observed criterion σ(I): -10 / Redundancy: 3 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.142 / Num. unique all: 2031 / % possible all: 75.4
Reflection
*PLUS
Num. obs: 24505 / % possible obs: 91.1 %
Reflection shell
*PLUS
% possible obs: 75.4 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→40.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 299506.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2418 9.9 %RANDOM
Rwork0.231 ---
all0.2352 26797 --
obs0.231 24505 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.379 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1--14.57 Å2-1.26 Å2-0.18 Å2
2--10.92 Å2-10.6 Å2
3---3.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.51→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4846 0 1 112 4959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.742
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.912.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 305 10 %
Rwork0.307 2753 -
obs--67.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 22087 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.13
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67

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