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- PDB-5izt: Crystal structure of a C-terminal proteolytic fragment of an oute... -

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Basic information

Entry
Database: PDB / ID: 5izt
TitleCrystal structure of a C-terminal proteolytic fragment of an outer surface protein from Borrelia burgdorferi
ComponentsOuter surface protein
KeywordsMEMBRANE PROTEIN / SSGCID / Borellia burgdorferi / Outer surface protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyBbcrasp-1 / Bbcrasp-1 / Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Orthogonal Bundle / Mainly Alpha / membrane / Outer surface protein
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a C-terminal proteolytic fragment of an outer surface protein from Borrelia burgdorferi
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer surface protein
B: Outer surface protein


Theoretical massNumber of molelcules
Total (without water)88,7912
Polymers88,7912
Non-polymers00
Water4,648258
1
A: Outer surface protein


Theoretical massNumber of molelcules
Total (without water)44,3951
Polymers44,3951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer surface protein


Theoretical massNumber of molelcules
Total (without water)44,3951
Polymers44,3951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.340, 54.030, 66.960
Angle α, β, γ (deg.)101.440, 98.730, 85.000
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 193 or (resid 194 and (name...
21(chain B and (resid 193:203 or resid 205:207 or resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain A and (resid 193 or (resid 194 and (name...AA193178
12LYSLYSLYSLYS(chain A and (resid 193 or (resid 194 and (name...AA194179
13SERSERMETMET(chain A and (resid 193 or (resid 194 and (name...AA193 - 411178 - 396
14SERSERMETMET(chain A and (resid 193 or (resid 194 and (name...AA193 - 411178 - 396
15SERSERMETMET(chain A and (resid 193 or (resid 194 and (name...AA193 - 411178 - 396
16SERSERMETMET(chain A and (resid 193 or (resid 194 and (name...AA193 - 411178 - 396
21SERSERILEILE(chain B and (resid 193:203 or resid 205:207 or resid...BB193 - 203178 - 188
22ALAALASERSER(chain B and (resid 193:203 or resid 205:207 or resid...BB205 - 207190 - 192
23GLUGLUGLNGLN(chain B and (resid 193:203 or resid 205:207 or resid...BB209 - 214194 - 199
24GLYGLYPHEPHE(chain B and (resid 193:203 or resid 205:207 or resid...BB218 - 233203 - 218
25LEULEUPROPRO(chain B and (resid 193:203 or resid 205:207 or resid...BB235 - 251220 - 236
26LEULEUARGARG(chain B and (resid 193:203 or resid 205:207 or resid...BB253 - 264238 - 249
27LYSLYSASPASP(chain B and (resid 193:203 or resid 205:207 or resid...BB266 - 274251 - 259
28TYRTYRTYRTYR(chain B and (resid 193:203 or resid 205:207 or resid...BB276261
29ILEILEILEILE(chain B and (resid 193:203 or resid 205:207 or resid...BB278263
210PHEPHEGLYGLY(chain B and (resid 193:203 or resid 205:207 or resid...BB281 - 282266 - 267
211ILEILEHISHIS(chain B and (resid 193:203 or resid 205:207 or resid...BB284 - 295269 - 280
212LEULEUILEILE(chain B and (resid 193:203 or resid 205:207 or resid...BB297 - 298282 - 283
213GLUGLULEULEU(chain B and (resid 193:203 or resid 205:207 or resid...BB300 - 301285 - 286
214ILEILEASNASN(chain B and (resid 193:203 or resid 205:207 or resid...BB303 - 336288 - 321
215PHEPHESERSER(chain B and (resid 193:203 or resid 205:207 or resid...BB338 - 362323 - 347
216GLNGLNALAALA(chain B and (resid 193:203 or resid 205:207 or resid...BB364 - 370349 - 355
217ALAALASERSER(chain B and (resid 193:203 or resid 205:207 or resid...BB372 - 374357 - 359
218SERSERMETMET(chain B and (resid 193:203 or resid 205:207 or resid...BB193 - 411178 - 396
219SERSERMETMET(chain B and (resid 193:203 or resid 205:207 or resid...BB193 - 411178 - 396
220SERSERMETMET(chain B and (resid 193:203 or resid 205:207 or resid...BB193 - 411178 - 396
221SERSERMETMET(chain B and (resid 193:203 or resid 205:207 or resid...BB193 - 411178 - 396

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Components

#1: Protein Outer surface protein


Mass: 44395.293 Da / Num. of mol.: 2 / Fragment: residues 24-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_A66 / Plasmid: BobuA.18967.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O50955
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Microlytic MCSG 1 screen H3: 20% PEG 4000, 20% iso-Propanol, 100mM Na3-citrate pH 5.6; BobuA.18967.a.B2.PW37767 at 20mg/ml; cryo: 20% EG; tray 266029 h3; puck rgo9-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 11, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 32761 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.92 % / Biso Wilson estimate: 23.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.18
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-1.950.4823.06196.3
1.95-20.3664.03196.7
2-2.060.2715.35197.1
2.06-2.120.2116.62196.9
2.12-2.190.1628.4197.2
2.19-2.270.1419.84197.2
2.27-2.360.11711.52197.6
2.36-2.450.09213.84197.5
2.45-2.560.08215.49198.2
2.56-2.690.06817.77198.1
2.69-2.830.05720.44198.5
2.83-30.04824.08198
3-3.210.0428.17198.4
3.21-3.470.03430.94198.6
3.47-3.80.03136.22199.1
3.8-4.250.02839.11198.8
4.25-4.910.02840.45198.7
4.91-6.010.0338.07199
6.01-8.50.02938.74199.1
8.5-500.02641.93195.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å45.4 Å
Translation2 Å45.4 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXmodel building
PHENIX(dev_2356)refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yn7

2yn7


Resolution: 1.9→27.405 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.72
RfactorNum. reflection% reflection
Rfree0.2113 2082 6.36 %
Rwork0.166 --
obs0.1688 32750 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.99 Å2 / Biso mean: 33.5274 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 1.9→27.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 0 260 3602
Biso mean---39.65 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063529
X-RAY DIFFRACTIONf_angle_d0.774767
X-RAY DIFFRACTIONf_chiral_restr0.046525
X-RAY DIFFRACTIONf_plane_restr0.004630
X-RAY DIFFRACTIONf_dihedral_angle_d15.2232248
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1597X-RAY DIFFRACTION5.268TORSIONAL
12B1597X-RAY DIFFRACTION5.268TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9002-1.94430.27321480.22392035218397
1.9443-1.9930.24821270.20422037216497
1.993-2.04680.24981360.18932029216597
2.0468-2.1070.21951610.18562004216597
2.107-2.1750.24421610.16882000216197
2.175-2.25270.19421340.16242053218797
2.2527-2.34290.1921260.15832033215998
2.3429-2.44940.22461360.16592055219198
2.4494-2.57850.22651470.16932043219098
2.5785-2.73990.24341300.17262044217498
2.7399-2.95120.17741390.17582045218498
2.9512-3.24780.2711190.17482090220999
3.2478-3.71680.20251340.15892076221099
3.7168-4.67890.1851490.14012052220199
4.6789-27.40750.18781350.16282072220799
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)
11.4037-2.2570.01927.7483-0.14120.1665-0.2087-0.24020.421-0.05180.3529-1.251-0.11950.1707-0.10950.2456-0.0594-0.05480.26020.00050.386113.4745-7.32725.4974
23.9606-0.73510.94112.6121-0.34463.1048-0.0208-0.08020.00450.3370.0388-0.2137-0.0887-0.0464-0.02050.1264-0.0241-0.02070.0786-0.00760.1336-2.35910.27043.4223
32.0833-2.80430.23755.992-0.94370.895-0.07350.0385-0.2050.1537-0.00940.06080.08790.06770.07240.1162-0.0305-0.01370.1218-0.03220.12652.3352-10.6584-0.0941
42.05672.1315-0.1565.3709-3.43763.40680.11070.47610.3476-0.1691-0.4086-0.6887-0.34270.2890.38580.87880.08980.29670.54950.36911.0582-5.487617.0602-17.4728
53.127-2.71381.21714.1352-2.86534.37410.24060.1516-0.3809-0.3858-0.0180.39040.2139-0.0522-0.21010.1318-0.0332-0.04650.1471-0.05490.1698-6.5578-2.8401-7.4289
63.3923-1.4503-0.54776.78880.11964.6880.04590.02260.9812-0.39270.0426-0.2707-0.41450.30970.00240.315-0.1086-0.04510.37150.16770.5991-6.95410.408323.4879
77.17582.3105-0.58196.0695-0.07237.17410.02851.09030.0048-1.41330.1588-0.51550.03670.4304-0.13920.54210.04790.07020.5097-0.03910.16496.7653-14.597819.5505
84.49610.57271.27093.64080.15144.49260.06190.3419-0.3671-0.2015-0.00610.07260.5266-0.0077-0.05810.22440.0217-0.00330.2388-0.04480.15053.205-18.077527.6139
95.0008-4.49071.50769.2406-2.01962.11790.05490.12950.0570.0324-0.00140.53380.0102-0.11790.00720.1354-0.06210.04410.2101-0.0130.1549-9.6588-5.990129.9788
104.0464-2.20551.31753.6627-0.80261.4851-0.3435-0.32360.63310.3670.17920.2649-0.3516-0.07710.22010.2339-0.0175-0.01820.1947-0.03020.3586-6.97014.023934.6528
115.3917-2.2772-0.44893.11150.22864.2183-0.2089-0.1222-0.5814-0.41290.90441.13520.6674-0.7281-0.57420.48030.0912-0.11810.76680.3071.168616.5563-19.568743.8374
122.9366-0.86583.14082.2052-2.13644.88490.1135-0.3709-0.20440.1495-0.0220.08460.1262-0.189-0.12250.1937-0.06410.03470.22030.00090.1154-3.7964-10.836141.6966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 193 through 223 )A193 - 223
2X-RAY DIFFRACTION2chain 'A' and (resid 224 through 291 )A224 - 291
3X-RAY DIFFRACTION3chain 'A' and (resid 292 through 374 )A292 - 374
4X-RAY DIFFRACTION4chain 'A' and (resid 375 through 380 )A375 - 380
5X-RAY DIFFRACTION5chain 'A' and (resid 381 through 411 )A381 - 411
6X-RAY DIFFRACTION6chain 'B' and (resid 193 through 213 )B193 - 213
7X-RAY DIFFRACTION7chain 'B' and (resid 214 through 225 )B214 - 225
8X-RAY DIFFRACTION8chain 'B' and (resid 226 through 291 )B226 - 291
9X-RAY DIFFRACTION9chain 'B' and (resid 292 through 331 )B292 - 331
10X-RAY DIFFRACTION10chain 'B' and (resid 332 through 372 )B332 - 372
11X-RAY DIFFRACTION11chain 'B' and (resid 373 through 380 )B373 - 380
12X-RAY DIFFRACTION12chain 'B' and (resid 381 through 411 )B381 - 411

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