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- PDB-4bod: Complement regulator acquiring outer surface protein BbCRASP-4 or... -

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Basic information

Entry
Database: PDB / ID: 4bod
TitleComplement regulator acquiring outer surface protein BbCRASP-4 or ErpC from Borrelia burgdorferi
ComponentsERPC
KeywordsCELL ADHESION / LIPOPROTEIN / COMPLEMENT FACTORS / OUTER SURFACE LIPOPROTEIN / LYME DISEASE
Function / homology
Function and homology information


Borrelia 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
Similarity search - Domain/homology
Biological speciesBORRELIA BURGDORFERI (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsBrangulis, K. / Petrovskis, I. / Kazaks, A. / 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 1.0May 28, 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: ERPC
B: ERPC


Theoretical massNumber of molelcules
Total (without water)34,9712
Polymers34,9712
Non-polymers00
Water00
1
A: ERPC


Theoretical massNumber of molelcules
Total (without water)17,4851
Polymers17,4851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ERPC


Theoretical massNumber of molelcules
Total (without water)17,4851
Polymers17,4851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.160, 71.160, 75.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein ERPC / CRASP-4


Mass: 17485.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BORRELIA BURGDORFERI (Lyme disease spirochete)
Strain: B31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44790

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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: 2.65 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 HEPES PH 7.5, 10% ISOPROPANOL, 20% PEG 6000

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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: Apr 19, 2013 / 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: 3.15→41.85 Å / Num. obs: 5659 / % possible obs: 86.3 % / Observed criterion σ(I): 1.7 / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.3
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 83.4

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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: 3.15→35.61 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 35.441 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 264 4.7 %RANDOM
Rwork0.1391 ---
obs0.14174 5393 85.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.137 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 3.15→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 0 0 2104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022130
X-RAY DIFFRACTIONr_bond_other_d0.0020.022019
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9592855
X-RAY DIFFRACTIONr_angle_other_deg0.72634663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0735259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01526.792106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51615404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.449152
X-RAY DIFFRACTIONr_chiral_restr0.0730.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
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_it7.2674.1381054
X-RAY DIFFRACTIONr_mcbond_other7.2264.1381053
X-RAY DIFFRACTIONr_mcangle_it9.5316.1841307
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.8074.5341076
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_restr4.63634149
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded23.80754123
LS refinement shellResolution: 3.151→3.233 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 24 -
Rwork0.302 380 -
obs--83.13 %

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