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- PDB-5a2u: Crystal structure of BBA68 or BbCRASP-1 from Borrelia burgdorferi... -

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Basic information

Entry
Database: PDB / ID: 5a2u
TitleCrystal structure of BBA68 or BbCRASP-1 from Borrelia burgdorferi strain B31
ComponentsCOMPLEMENT REGULATOR ACQUIRING PROTEIN 1
KeywordsIMMUNE SYSTEM / LYME DISEASE / LIPOPROTEIN / OUTER SURFACE PROTEIN
Function / homologyBbcrasp-1 / Bbcrasp-1 / Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Orthogonal Bundle / Mainly Alpha / Complement regulator-acquiring surface protein 1 (CRASP-1) / Complement regulator acquiring protein 1
Function and homology information
Biological speciesBORRELIA BURGDORFERI (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBrangulis, K. / Bertulis, E. / Petrovskis, I. / Kazaks, A. / Tars, K.
CitationJournal: To be Published
Title: Crystal Structure of Bba68 or Bbcrasp-1 from Borrelia Burgdorferi Strain B31
Authors: Brangulis, K. / Petrovskis, I. / Kazaks, A. / Tars, K.
History
DepositionMay 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMPLEMENT REGULATOR ACQUIRING PROTEIN 1
B: COMPLEMENT REGULATOR ACQUIRING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)45,1522
Polymers45,1522
Non-polymers00
Water00
1
B: COMPLEMENT REGULATOR ACQUIRING PROTEIN 1

B: COMPLEMENT REGULATOR ACQUIRING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)45,1522
Polymers45,1522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/41
Buried area4660 Å2
ΔGint-37.7 kcal/mol
Surface area19830 Å2
MethodPISA
2
A: COMPLEMENT REGULATOR ACQUIRING PROTEIN 1

A: COMPLEMENT REGULATOR ACQUIRING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)45,1522
Polymers45,1522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4550 Å2
ΔGint-30.4 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 54.630, 394.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein COMPLEMENT REGULATOR ACQUIRING PROTEIN 1 / BBA68 OR BBCRASP-1


Mass: 22575.879 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 65-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BORRELIA BURGDORFERI (Lyme disease spirochete)
Strain: B31 / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q66ZA0, UniProt: O50957*PLUS

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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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 8 / Details: 10% PEG 10 000 0.1M TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.0688
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: RH-COATED TOROIDAL SI MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0688 Å / Relative weight: 1
ReflectionResolution: 3.3→56.33 Å / Num. obs: 9488 / % possible obs: 96.9 % / Observed criterion σ(I): 2.4 / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.9
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W33

1w33


Resolution: 3.3→50.45 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.919 / SU B: 22.749 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28643 441 4.7 %RANDOM
Rwork0.24602 ---
obs0.24795 8961 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.414 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 0 0 2973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193009
X-RAY DIFFRACTIONr_bond_other_d0.0020.023003
X-RAY DIFFRACTIONr_angle_refined_deg1.9981.9764024
X-RAY DIFFRACTIONr_angle_other_deg1.04636957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28126.863153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.44715654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.008155
X-RAY DIFFRACTIONr_chiral_restr0.1730.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02639
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.4139.7641416
X-RAY DIFFRACTIONr_mcbond_other6.4139.7621415
X-RAY DIFFRACTIONr_mcangle_it9.93714.6451763
X-RAY DIFFRACTIONr_mcangle_other9.93514.6461764
X-RAY DIFFRACTIONr_scbond_it6.67710.4141592
X-RAY DIFFRACTIONr_scbond_other6.67510.4151593
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.78115.3372262
X-RAY DIFFRACTIONr_long_range_B_refined15.81992.84412748
X-RAY DIFFRACTIONr_long_range_B_other15.81992.84612749
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 34 -
Rwork0.308 673 -
obs--97.92 %

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