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- PDB-7zjj: CspZ (BbCRASP-2) from Borrelia burgdorferi strain B379 -

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Basic information

Entry
Database: PDB / ID: 7zjj
TitleCspZ (BbCRASP-2) from Borrelia burgdorferi strain B379
ComponentsCspZ
KeywordsMEMBRANE PROTEIN / Lyme disease / borreliosis / outer surface protein / BBH06 / complement binding.
Function / homologyNITRATE ION
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBrangulis, K. / Marcinkiewicz, A. / Hart, T.M. / Dupuis, A.P. / Zamba Campero, M. / Nowak, T.A. / Stout, J.L. / Akopjana, I. / Kazaks, A. / Bogans, J. ...Brangulis, K. / Marcinkiewicz, A. / Hart, T.M. / Dupuis, A.P. / Zamba Campero, M. / Nowak, T.A. / Stout, J.L. / Akopjana, I. / Kazaks, A. / Bogans, J. / Ciota, A.T. / Kraiczy, P. / Kolokotronis, S.O. / Lin, Y.-P.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other governmentlzp-2020/2-0378 Latvia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural evolution of an immune evasion determinant shapes pathogen host tropism.
Authors: Marcinkiewicz, A.L. / Brangulis, K. / Dupuis 2nd, A.P. / Hart, T.M. / Zamba-Campero, M. / Nowak, T.A. / Stout, J.L. / Akopjana, I. / Kazaks, A. / Bogans, J. / Ciota, A.T. / Kraiczy, P. / ...Authors: Marcinkiewicz, A.L. / Brangulis, K. / Dupuis 2nd, A.P. / Hart, T.M. / Zamba-Campero, M. / Nowak, T.A. / Stout, J.L. / Akopjana, I. / Kazaks, A. / Bogans, J. / Ciota, A.T. / Kraiczy, P. / Kolokotronis, S.O. / Lin, Y.P.
History
DepositionApr 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CspZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5352
Polymers25,4731
Non-polymers621
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint1 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.597, 59.950, 61.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein CspZ


Mass: 25473.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First 4 residues (GAMG) are remnants from the expression tag after TEV protease cleavage. C-terminal region only.
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Strain: B379 / Gene: cspZ / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammonium citrate 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→61.05 Å / Num. obs: 11805 / % possible obs: 98.9 % / Redundancy: 10.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 952 / CC1/2: 0.985

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CBE

4cbe


Resolution: 2.1→42.81 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.092 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 594 5 %RANDOM
Rwork0.2086 ---
obs0.2113 11190 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.36 Å2 / Biso mean: 31.647 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å2-0 Å2
2--0.4 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: final / Resolution: 2.1→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 4 111 1884
Biso mean--31.84 30.99 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131797
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161757
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.6372409
X-RAY DIFFRACTIONr_angle_other_deg1.3631.5934057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67724.30193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26315359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.42157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 34 -
Rwork0.371 823 -
all-857 -
obs--99.08 %

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