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- PDB-4bob: Structure of Complement regulator-acquiring surface protein 3 (CR... -

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Basic information

Entry
Database: PDB / ID: 4bob
TitleStructure of Complement regulator-acquiring surface protein 3 (CRASP- 3, ErpP or BBN38) from Borrelia burgdorferi
ComponentsERPP PROTEIN
KeywordsCELL ADHESION / LIPOPROTEIN / COMPLEMENT FACTORS / OUTER SURFACE LIPOPROTEIN / LYME DISEASE
Function / homologyBorrelia outer surface protein E/F / OspE-like superfamily / Borrelia outer surface protein E / Borrelia outer surface protein E/F / Transcriptional Co-activator pc4; Chain A / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Mainly Beta / ErpP protein
Function and homology information
Biological speciesBORRELIA BURGDORFERI (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsBrangulis, K. / Petrovskis, I. / Baumanis, V. / Tars, K.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Crystal Structures of the Erp Protein Family Members Erpp and Erpc from Borrelia Burgdorferi Reveal the Reason for Different Affinities for Complement Regulator Factor H.
Authors: Brangulis, K. / Petrovskis, I. / Kazaks, A. / Akopjana, I. / Tars, K.
History
DepositionMay 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: 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: ERPP PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,0561
Polymers18,0561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.030, 55.130, 81.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ERPP PROTEIN / ERPP / BBN38


Mass: 18056.109 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-186
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: Q9S036

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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: 1.68 Å3/Da / Density % sol: 27 % / Description: NONE
Crystal growpH: 7.5 / Details: 28% PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2012 / 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 Å / Relative weight: 1
ReflectionResolution: 2.53→32.74 Å / Num. obs: 3927 / % possible obs: 90.5 % / Observed criterion σ(I): 2.7 / Redundancy: 2.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.7
Reflection shellResolution: 2.53→2.67 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.5 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4J38

4j38


Resolution: 2.53→32.74 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.894 / SU B: 23.89 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26087 186 4.8 %RANDOM
Rwork0.23482 ---
obs0.2362 3723 88.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.436 Å2
Baniso -1Baniso -2Baniso -3
1--4.71 Å20 Å20 Å2
2---13.68 Å20 Å2
3---18.39 Å2
Refinement stepCycle: LAST / Resolution: 2.53→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 0 0 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191050
X-RAY DIFFRACTIONr_bond_other_d0.0010.021018
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9511405
X-RAY DIFFRACTIONr_angle_other_deg0.82932355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9495130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26926.45848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.52215203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg35.771151
X-RAY DIFFRACTIONr_chiral_restr0.0910.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
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_it2.0021.671526
X-RAY DIFFRACTIONr_mcbond_other1.991.671525
X-RAY DIFFRACTIONr_mcangle_it2.5372.491654
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0121.787524
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.24732068
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded5.6652053
LS refinement shellResolution: 2.53→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.668 10 -
Rwork0.407 253 -
obs--84.29 %

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