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Basic information

Entry
Database: PDB / ID: 9jsa
TitleCatPSAM-H8
ComponentsOuter Surface Protein A
KeywordsPROTEIN BINDING / OspA / outer surface protein A
Function / homologyOuter surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Outer Surface Protein A
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMakabe, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H01873 Japan
CitationJournal: To Be Published
Title: CatPSAM-H8
Authors: Makabe, K.
History
DepositionSep 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)68,9402
Polymers68,9402
Non-polymers00
Water4,576254
1
A: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)34,4701
Polymers34,4701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer Surface Protein A


Theoretical massNumber of molelcules
Total (without water)34,4701
Polymers34,4701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.205, 79.450, 227.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Outer Surface Protein A


Mass: 34470.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Production host: Escherichia coli (E. coli) / References: UniProt: D0VWU8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH7.5, 25% v/v PEG Smear Medium, protein 10.14 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→46.21 Å / Num. obs: 41886 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 38.83 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14
Reflection shellResolution: 2.06→2.12 Å / Rmerge(I) obs: 1.004 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 33997

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREPphasing
PHENIX1.171refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / SU ML: 0.2932 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2054
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2883 1757 5.11 %
Rwork0.2632 32660 -
obs0.2645 34417 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 0 254 5010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00494796
X-RAY DIFFRACTIONf_angle_d0.87786438
X-RAY DIFFRACTIONf_chiral_restr0.0492776
X-RAY DIFFRACTIONf_plane_restr0.0041814
X-RAY DIFFRACTIONf_dihedral_angle_d21.45481804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.34841360.34062488X-RAY DIFFRACTION99.96
2.26-2.330.36011390.32832440X-RAY DIFFRACTION100
2.33-2.40.37111400.32362484X-RAY DIFFRACTION100
2.4-2.490.35711220.32372454X-RAY DIFFRACTION99.81
2.49-2.590.33681230.32372524X-RAY DIFFRACTION99.96
2.59-2.70.46261260.33242437X-RAY DIFFRACTION99.92
2.7-2.850.36561220.33072502X-RAY DIFFRACTION99.89
2.85-3.020.29781510.30472506X-RAY DIFFRACTION99.89
3.02-3.260.3281310.30052490X-RAY DIFFRACTION99.96
3.26-3.580.26991430.26452510X-RAY DIFFRACTION100
3.58-4.10.26671260.2372556X-RAY DIFFRACTION100
4.1-5.150.22191490.19092573X-RAY DIFFRACTION99.93
5.15-200.2491490.22412696X-RAY DIFFRACTION99.93
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)
14.651009740910.483008894607-0.4157859229553.68983422532-0.4363620344174.73289699079-0.07150600712731.50384604028-0.0399327612139-1.50848577734-0.0002309525541560.1399128584030.325544710006-0.1591830485730.05402603242150.8611543955070.119669823624-0.02432147297680.673792822836-0.03038680361590.3472318900825.67928335492-24.563824965-37.8234333815
21.33212798828-0.287185813253-0.1644871948281.858064451042.310562441614.14632503764-0.004026907320050.1206650373440.00355354825979-0.0541918174509-0.08658065033480.049489344148-0.00296119251387-0.01120162018040.08406037021840.205088385974-0.0170353312983-0.004157372770960.1784383564620.01761378221820.2849577487135.05047501208-9.65328470230.129936236029
35.425743396740.134010754880.7438169088493.9291147808-1.35757795817.04725074487-0.07208768962450.06920200100070.635745992244-0.0986249991163-0.01227114421240.349588049927-0.958137780242-0.5735359113420.07805243872780.4155544339750.0282345385299-0.08719756802350.36939976177-0.02774598044470.3805748955390.04133974308289.19159586053-11.9950742491
40.983401171842-0.674539748269-1.509744254992.133475102351.538398620443.83977619241-0.180394955054-0.7423739931710.003293081644480.4040449318140.185786463444-0.2841028621220.4611811666521.06228766603-0.007679374057780.7516318030660.0785158505964-0.0166516438830.879989467780.06605564534410.41427777676219.5400465902-6.36387546568-43.9969832295
54.83957520082-1.05691899877-0.3713199800325.46902085987-1.036033173056.09275528669-0.300428621030.000642585136383-0.529278074728-0.124806719203-0.1464791903240.09844883948231.32734739903-0.2175854718250.4511276034670.634273069624-0.05111269974290.09392349364950.3514965713310.0329776516850.35667584711415.720632141-17.7437144114-73.3679566965
63.431700443050.0948132858524-0.3774667527233.161018707920.7712656732114.38645551659-0.00247207290437-0.295785722680.4076041050040.0311421778431-0.1967092607430.645107928727-0.24175192988-0.3358846297480.1829530502480.22129455323-0.0326139560953-0.004484969494960.258850467292-0.09995141223090.422106219068-13.46869710363.2198299439322.2764210801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 251 )
3X-RAY DIFFRACTION3chain 'B' and (resid 28 through 138 )
4X-RAY DIFFRACTION4chain 'B' and (resid 139 through 251 )
5X-RAY DIFFRACTION5chain 'B' and (resid 252 through 342 )
6X-RAY DIFFRACTION6chain 'A' and (resid 252 through 342 )

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