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- PDB-7uj6: Outer Surface Protein C Type K -

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Basic information

Entry
Database: PDB / ID: 7uj6
TitleOuter Surface Protein C Type K
ComponentsOuter surface protein C
KeywordsUNKNOWN FUNCTION / Outer Surface Protein Borrelia Burgdorferi
Function / homologyLipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Outer surface protein C
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsRudolph, M.J. / Mantis, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00040 United States
CitationJournal: Mbio / Year: 2023
Title: Structural Elucidation of a Protective B Cell Epitope on Outer Surface Protein C (OspC) of the Lyme Disease Spirochete, Borreliella burgdorferi.
Authors: Rudolph, M.J. / Davis, S.A. / Haque, H.M.E. / Weis, D.D. / Vance, D.J. / Piazza, C.L. / Ejemel, M. / Cavacini, L. / Wang, Y. / Mbow, M.L. / Gilmore, R.D. / Mantis, N.J.
History
DepositionMar 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)70,6054
Polymers70,6054
Non-polymers00
Water6,449358
1
A: Outer surface protein C
B: Outer surface protein C


Theoretical massNumber of molelcules
Total (without water)35,3032
Polymers35,3032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-40 kcal/mol
Surface area14100 Å2
MethodPISA
2
C: Outer surface protein C
D: Outer surface protein C


Theoretical massNumber of molelcules
Total (without water)35,3032
Polymers35,3032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-42 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.316, 52.343, 116.682
Angle α, β, γ (deg.)90.000, 92.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 42 through 67 or resid 69...
21(chain B and (resid 42 through 67 or resid 69...
31(chain C and (resid 42 through 67 or resid 69...
41(chain D and (resid 42 through 67 or resid 69...

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
11LEULEUALAALA(chain A and (resid 42 through 67 or resid 69...AA42 - 675 - 30
12ILEILEGLYGLY(chain A and (resid 42 through 67 or resid 69...AA69 - 9532 - 58
13LEULEULEULEU(chain A and (resid 42 through 67 or resid 69...AA97 - 11560 - 78
14GLUGLUALAALA(chain A and (resid 42 through 67 or resid 69...AA119 - 14482 - 107
15LEULEULYSLYS(chain A and (resid 42 through 67 or resid 69...AA42 - 1975 - 160
16VALVALALAALA(chain A and (resid 42 through 67 or resid 69...AA151 - 166114 - 129
17ASPASPVALVAL(chain A and (resid 42 through 67 or resid 69...AA168 - 196131 - 159
21LEULEUALAALA(chain B and (resid 42 through 67 or resid 69...BB42 - 675 - 30
22ILEILEGLYGLY(chain B and (resid 42 through 67 or resid 69...BB69 - 9532 - 58
23LEULEULEULEU(chain B and (resid 42 through 67 or resid 69...BB97 - 11560 - 78
24LEULEUVALVAL(chain B and (resid 42 through 67 or resid 69...BB42 - 1965 - 159
25VALVALALAALA(chain B and (resid 42 through 67 or resid 69...BB151 - 166114 - 129
26VALVALALAALA(chain B and (resid 42 through 67 or resid 69...BB151 - 166114 - 129
27ASPASPVALVAL(chain B and (resid 42 through 67 or resid 69...BB168 - 196131 - 159
31LEULEUALAALA(chain C and (resid 42 through 67 or resid 69...CC42 - 675 - 30
32ILEILEGLYGLY(chain C and (resid 42 through 67 or resid 69...CC69 - 9532 - 58
33LEULEUALAALA(chain C and (resid 42 through 67 or resid 69...CC97 - 14460 - 107
34LEULEUGLUGLU(chain C and (resid 42 through 67 or resid 69...CC146 - 149109 - 112
35VALVALALAALA(chain C and (resid 42 through 67 or resid 69...CC151 - 166114 - 129
36ASPASPVALVAL(chain C and (resid 42 through 67 or resid 69...CC168 - 196131 - 159
41LEULEUALAALA(chain D and (resid 42 through 67 or resid 69...DD42 - 675 - 30
42ILEILEGLYGLY(chain D and (resid 42 through 67 or resid 69...DD69 - 9532 - 58
43LEULEUALAALA(chain D and (resid 42 through 67 or resid 69...DD97 - 14460 - 107
44LEULEUGLUGLU(chain D and (resid 42 through 67 or resid 69...DD146 - 149109 - 112
45VALVALALAALA(chain D and (resid 42 through 67 or resid 69...DD151 - 166114 - 129
46ASPASPVALVAL(chain D and (resid 42 through 67 or resid 69...DD168 - 196131 - 159

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Components

#1: Protein
Outer surface protein C


Mass: 17651.326 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Type K
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Strain: 297 / Gene: ospC, Bbu297_B19 / Production host: Escherichia coli (E. coli) / References: UniProt: E4QRR2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 40% PEG 400, 200 mM Li2SO4, 10 mM 2-Aminoethanesulfonic acid.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 45203 / % possible obs: 97.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.071 / Rrim(I) all: 0.165 / Χ2: 1.149 / Net I/σ(I): 6.1 / Num. measured all: 237937
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.9851.31122330.5350.6391.4640.32799.2
1.98-2.025.31.01722870.630.491.1330.35498.7
2.02-2.065.50.85522740.7850.4070.950.38899
2.06-2.15.50.69222770.8260.3280.7680.42798.8
2.1-2.155.60.57422100.8840.270.6360.46798.7
2.15-2.25.60.4923260.9040.2310.5430.48598.9
2.2-2.255.50.40122600.8980.1930.4460.59198.5
2.25-2.315.40.33422590.9470.160.3720.65398.6
2.31-2.385.30.27722950.9570.1370.3110.68699
2.38-2.465.20.25122370.9690.1240.2810.77398.7
2.46-2.5450.22722930.9670.1120.2540.80898.5
2.54-2.654.80.20322500.970.1010.2280.95397.5
2.65-2.774.20.16222040.970.0870.1851.20395.5
2.77-2.915.20.15522900.9840.0750.1731.38198.6
2.91-3.15.50.13522540.9870.0630.151.74897.6
3.1-3.335.50.10822690.9910.050.1192.15998.4
3.33-3.675.40.08922520.9930.0410.0982.43697.1
3.67-4.250.07222000.9940.0350.0812.48794.8
4.2-5.294.60.06421470.9940.0320.0722.43590.1
5.29-5060.05423860.9980.0240.0592.31799

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GGQ
Resolution: 1.951→39.782 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 2184 4.84 %
Rwork0.1929 42973 -
obs0.1945 45157 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.96 Å2 / Biso mean: 44.7944 Å2 / Biso min: 13.91 Å2
Refinement stepCycle: final / Resolution: 1.951→39.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4656 0 0 358 5014
Biso mean---41.28 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034727
X-RAY DIFFRACTIONf_angle_d0.5176332
X-RAY DIFFRACTIONf_chiral_restr0.036786
X-RAY DIFFRACTIONf_plane_restr0.003796
X-RAY DIFFRACTIONf_dihedral_angle_d10.4972992
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2765X-RAY DIFFRACTION8.159TORSIONAL
12B2765X-RAY DIFFRACTION8.159TORSIONAL
13C2765X-RAY DIFFRACTION8.159TORSIONAL
14D2765X-RAY DIFFRACTION8.159TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9511-1.99350.31061520.2653264898
1.9935-2.03990.26151460.2295267599
2.0399-2.09090.22251420.2095273298
2.0909-2.14740.22211340.192262699
2.1474-2.21060.23791540.1891272299
2.2106-2.28190.26631210.1859271699
2.2819-2.36350.2361210.1869270199
2.3635-2.45810.23091430.1855269499
2.4581-2.56990.22421490.199267998
2.5699-2.70540.24991090.2002269597
2.7054-2.87490.23931180.1917268397
2.8749-3.09680.27321390.1988271898
3.0968-3.40820.2411210.1913269198
3.4082-3.90110.20151430.1725268497
3.9011-4.91350.19311510.1774254092
4.9135-39.7820.21671410.2041276997
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.64150.57460.94752.04010.34025.4004-0.2283-0.80390.04140.7709-0.0405-0.2724-0.04010.12750.2540.41510.0544-0.01390.46430.01560.268321.8257-53.893436.9786
23.1570.3525-0.77363.8299-1.10382.8587-0.0157-0.18970.06790.1552-0.0215-0.25280.05550.0210.04590.0759-0.0119-0.03440.1720.00330.322621.5629-52.122217.774
33.54850.7082-2.43814.2182-1.27674.69630.1052-0.5776-0.59120.7696-0.2586-0.03440.8980.0070.24560.3648-0.0759-0.00110.27030.11230.459113.6366-65.25625.0109
44.3753-2.2285-1.88725.74342.53387.71560.07980.4059-0.41780.0497-0.24190.1220.0379-0.39590.15510.0866-0.0393-0.01510.1754-0.00510.299311.6333-54.30389.3685
54.39471.28763.34413.87312.24552.6545-0.1751-1.3298-0.12941.0554-0.03790.14450.2306-1.15380.25780.45840.04720.03710.53790.05910.309512.2694-55.772436.1063
62.8856-0.2787-0.89223.152-0.08582.3218-0.1027-1.02180.24730.793-0.03740.2039-0.06810.21310.24090.3947-0.0090.00180.6018-0.12540.41426.6664-47.909237.1341
75.44546.04290.15659.165-1.65532.0621-0.19620.5108-0.5852-0.42250.0164-0.01640.44370.0350.1110.1947-0.02570.04980.2415-0.1010.450725.8413-59.64177.0345
84.58311.92182.63963.18841.99818.43710.0358-0.31260.83310.2083-0.14550.0669-0.3004-0.21720.20020.13970.0117-0.01160.1692-0.03540.472225.3857-41.257820.9974
93.48141.85944.04378.18410.89794.9239-0.371-2.14531.07012.3656-0.032-0.1564-1.63550.75120.32770.981-0.08830.02051.4078-0.3840.47530.4808-35.774541.832
101.67120.0402-0.68680.98-0.47594.34630.1151-0.43070.4660.20440.2208-0.1003-1.22210.525-0.30880.3065-0.0231-0.01640.2905-0.14090.630634.299-35.712725.8289
112.2662-0.6823-3.98592.2818-0.49478.430.17770.48911.0015-0.4849-0.1610.3253-0.3305-0.3406-0.09820.13580.03950.01950.2280.10620.501431.4118-42.13564.435
123.12092.08922.5612.4181-0.67019.0163-0.06530.12420.1937-0.0522-0.1788-0.58350.22290.90970.07180.14290.00390.01840.22510.02690.545239.0023-47.618312.3504
135.99521.391-6.7914.8079-2.37336.967-0.3138-1.72340.24411.046-0.0287-0.0020.31312.11150.22750.42930.0874-0.06440.6722-0.11740.509736.2315-45.630335.2239
142.78810.15610.40643.07220.38412.5738-0.0488-0.86910.11251.0395-0.24870.09380.3257-0.07010.27780.58840.00720.05390.4009-0.05320.3276-6.2926-21.218137.521
157.7805-3.26991.4411.8615-0.60982.1376-0.40910.5561-0.2956-0.58140.3091-0.9619-0.62120.46240.01470.0391-0.01830.13740.2519-0.05340.64277.8226-21.6988.0747
165.448-1.8381-4.51063.59662.76274.1558-0.1594-0.0147-0.19020.3538-0.12490.35080.5629-0.34020.29750.2131-0.03440.03150.1688-0.02940.3385-11.5634-22.269120.6161
176.5378-1.7602-2.72446.56546.81068.0577-0.1875-1.9391-0.19652.3354-0.78491.59240.9409-1.73160.95430.74790.03380.08840.8673-0.08980.5145-17.4604-16.571940.4483
182.9086-0.6995-1.25473.40560.7364.36550.0384-0.23430.27960.5349-0.11960.41450.0336-1.00560.11680.2315-0.01260.06450.2504-0.07560.5098-17.3527-13.305725.0477
191.50990.65620.02075.03253.45696.6738-0.00380.06240.4343-0.2184-0.17380.197-0.3583-0.23350.09790.13570.02320.00260.15620.01410.4191-6.5827-11.37839.6723
202.9322-0.38231.67724.2771-2.94022.6407-0.1415-0.77430.05991.4791-0.26350.0601-1.34320.12960.36690.5782-0.01350.03340.4206-0.08260.3645-7.7577-12.207538.5777
213.49080.37621.67793.04411.79058.0192-0.2356-0.79380.24350.9275-0.37960.1620.1577-0.67710.49380.47830.0211-0.0140.3186-0.01040.3541-0.5171-26.330637.0429
224.37390.00612.02192.8345-0.70034.1493-0.0162-0.18140.12670.2305-0.0812-0.1252-0.0787-0.05640.08130.19810.00160.02920.0733-0.04450.3293-0.8223-26.108417.6715
232.7479-0.4339-0.29453.12870.68562.40290.0138-0.3784-0.09940.80620.3125-0.75440.2840.8326-0.27840.33950.0594-0.15760.2942-0.040.644611.9446-34.136126.2609
244.88710.1321-1.71422.6682-1.96848.7689-0.13480.0147-0.547-0.1265-0.0551-0.39940.25630.0160.14330.14430.01570.01560.1147-0.05040.41632.3266-35.92899.7725
255.0233-1.369-3.6243.61823.01083.4537-0.4424-0.9514-0.38441.7809-0.0477-0.09141.47070.33850.62960.86860.0241-0.03060.39110.05460.38920.9591-35.255438.739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 75 )A42 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 121 )A76 - 121
3X-RAY DIFFRACTION3chain 'A' and (resid 122 through 141 )A122 - 141
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 170 )A142 - 170
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 197 )A171 - 197
6X-RAY DIFFRACTION6chain 'B' and (resid 42 through 75 )B42 - 75
7X-RAY DIFFRACTION7chain 'B' and (resid 76 through 94 )B76 - 94
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 113 )B95 - 113
9X-RAY DIFFRACTION9chain 'B' and (resid 114 through 121 )B114 - 121
10X-RAY DIFFRACTION10chain 'B' and (resid 122 through 141 )B122 - 141
11X-RAY DIFFRACTION11chain 'B' and (resid 142 through 152 )B142 - 152
12X-RAY DIFFRACTION12chain 'B' and (resid 153 through 170 )B153 - 170
13X-RAY DIFFRACTION13chain 'B' and (resid 171 through 196 )B171 - 196
14X-RAY DIFFRACTION14chain 'C' and (resid 41 through 75 )C41 - 75
15X-RAY DIFFRACTION15chain 'C' and (resid 76 through 94 )C76 - 94
16X-RAY DIFFRACTION16chain 'C' and (resid 95 through 113 )C95 - 113
17X-RAY DIFFRACTION17chain 'C' and (resid 114 through 121 )C114 - 121
18X-RAY DIFFRACTION18chain 'C' and (resid 122 through 141 )C122 - 141
19X-RAY DIFFRACTION19chain 'C' and (resid 142 through 170 )C142 - 170
20X-RAY DIFFRACTION20chain 'C' and (resid 171 through 200 )C171 - 200
21X-RAY DIFFRACTION21chain 'D' and (resid 42 through 75 )D42 - 75
22X-RAY DIFFRACTION22chain 'D' and (resid 76 through 121 )D76 - 121
23X-RAY DIFFRACTION23chain 'D' and (resid 122 through 141 )D122 - 141
24X-RAY DIFFRACTION24chain 'D' and (resid 142 through 170 )D142 - 170
25X-RAY DIFFRACTION25chain 'D' and (resid 171 through 200 )D171 - 200

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